"It was all very well going on about pure logic and how the universe was ruled by logic and the harmony of numbers, but the plain fact of the matter was that the Disc was manifestly traversing space on the back of a giant turtle and the gods had a habit of going round to atheists' houses and smashing their windows."
Atheism in a clockwork universe ostensibly overseen by a completely non-interventionist divinity is one thing, but what about a world that's practically the playground of the mythic forces that created it?
While some authors do this as an honest philosophical exercise, it's pretty much always done for laughs. A self-styled hardline atheist that just happens to live in a high fantasy setting brimming with both huge pantheons of gods rampaging around the landscape constantly causing all sorts of things to happen, and the worshipers that pray to (and immediately hear back from) said pantheons of rampaging deities. Maybe they don't believe in the gods at all, and are totally nuts, maybe they're completely in denial about the existence of gods, or maybe they're feigning disbelief in hopes of ending their worship and bringing about some kind of Götterdämmerung or whatever. Sometimes the character himself is a god (typically a loony one). Sometimes this is a direct attempt to discredit science by comparing it to religion: Instead of using the scientific method, as a scientist does, the strawman atheist relies himself on a devout faith — in this case a faith that "science" holds all the answers, despite obvious proof to the contrary.
The trope can be justified in some ways. It's relatively common to have a character who openly acknowledges the existence of beings of great power, but refuses to accept their divinity (either because he believes them to be Sufficiently Advanced Aliens using technological trickery, or because he differentiates between a "real" god and a supernatural being that is merely very powerful). For instance, in The DCU (see below) there's no practical difference between, say, angels and alien energy beings. The main difference often comes down to whether or not the subject in question has deep personal implications, like an afterlife. On the other hand, in a world where magic is commonly known to be real, it becomes a lot easier for con artists to pull the wool over the eyes of innocents, so a skeptic to differentiate between "real" magic and "fake" magic can come in handy.
After a certain point, however, it can devolve into semantics, and you can start to wonder what exactly a character defines a god or magic as, especially considering some of the entities they encounter are even more powerful than most gods of myth.
A subtrope of this is the atheist who's plucked out of the normal world and forced to acknowledge the existence of the supernatural, usually only accepting it after something wildly impossible is done to them (like being turned into a dragon and back in C. S. Lewis' The Voyage of the Dawn Treader or having the flesh burned off his bones and regrown in Niven and Pournelle's Inferno) (even then, it took a long time for the protagonist to drop the idea that it was a theme park for sadistic sufficiently advanced aliens).
Compare with Agent Scully; Magic Versus Science; No Such Thing as Space Jesus; and No Such Thing as Wizard Jesus. See also Crossover Cosmology and Negative Continuity for two possible justifications, along with Arbitrary Skepticism, God Test, and Grumpy Bear. Sometimes one too many strange things happening will lead these characters into Giving Up On Logic.
Don't confuse this with the Nay-Theist, who knows supernatural forces exist, but thinks they should mind their own business and leave mortals alone. The trope name comes from the once-common belief that the Earth was flat instead of spherical.note …which some people still believe today. Also compare Eskimos Aren't Real, which is when a character does not believe in something that everyone else believes, but may in fact have never seen it.
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Anime and Manga
In One Piece's Skypeia arc, Zoro says he doesn't believe in God. Considering the main enemy in that arc is apparently God it's later revealed that he isn't, and it's just a title for the ruler of Skypeia.
Devil Fruits are regarded as mythical in certain parts of the East Blue. While devil fruits and their users are rare, especially outside of the Grand Line (where the main adventure takes place), most of the world's most prominent military figures and the most widely known and feared pirates do possess devil fruit powers, and there is known scientific literature seemingly available to the general public describing devil fruits and their effects.
Seto Kaiba in Yu-Gi-Oh! says Screw Destiny to the long history of Duel Monsters and of his rivalry with Yugi, even when he is told outright and went through the entire Millennium World arc. He goes on to found Duel Academia, a school existing solely for the purpose of being a roach motel for Eldritch Abominations, but not until the main Yu-Gi-Oh series itself is over.
Kaiba reaches levels of this where he's a damn near parody. In the filler arc, he and Yugi are fighting monster spirits outside of duels, and despite the fact that this crazy stuff is happening right in front of him, he's still adamant that it's all a magic trick that Yugi is doing.
Kaiba's denial of magic is far more pronounced in the English dub by 4Kids. In the original, it didn't take him long to get to the point that he recognized that magic is real. He just didn't care. Whether there was a historic and magical importance to Duel Monsters didn't matter to him, winning at it did.
Ishizu: (after using magical powers to show him a vision of the past) Now do you believe me, Kaiba?
Kaiba: Since I'm the most skeptical person on the planet, I'm going to say no.
Mr. Satan/Hercule of Dragon Ball Z was completely oblivious that the superpowered main characters were stronger than him, thinking it all to be a trick (he doesn't appear to have done the research on Roshi, Tien, and Goku, all of whom were champions of previous editions of the World Martial Arts Tournament that Mr. Satan rose to fame by winning) and later on a dream. Toward the end of the Cell saga, he seems to be trying to convince himself that it's not real. After the Cell saga, it becomes a Kayfabe put up by Goku and his fellows. Mr. Satan ends up bribing Android 18 to throw a fight against him so as to maintain the illusion that he's the strongest. By the end of the series, with, among other things, holding the leash of an ice cream-loving Eldritch Abomination and his beloved daughter marrying the strongest man on the planet, he's fully in the know but helps maintain The Masquerade so as to keep the general population blissfully unaware of the constant danger they're usually in.
One of the hardest things for newcomers to Umineko: When They Cry to get their heads around is that the main character is having a very intense and logical debate denying the existence of a witch that haunts his family's mansion... with the witch in question. And his only tools in this debate? The magic textshe grants to him. (In episode 6, however, he's part of the pro-witch side, since he's the new GM.)
This starts making a lot more sense as the story goes on. By the fourth arc, he's not fighting to deny magic in itself but the fact that the murders were committed by that witch. By the fifth, there's another witch who brings in a piece to do the same thing (in her words, "dispel the Illusion of the witch"), though in a some different and more brutal way.
It's not so much that Battler can't believe, but he can't allow the existence of someone so cruel. This backs him into a corner logically; he can't accept a strange, malevolent force but he also can't accept that it could be done by any member of his family or household. He refuses the witch, but also refuses to logically counter by accusing a culprit.
Seikimatsu Occult Gakuin has Maya, who is constantly assaulted by occult forces, yet for most of the series continues to loudly deny their existence - even while being attacked by a zombie in the first episode. She is often described as tsundere for the occult (even in the series itself once or twice), particularly since despite her (backstory-related) hatred of the occult, she is practically a walking encyclopedia on the subject, and is usually the one explaining occult concepts to the other characters. It's no surprise that people keep pairing her with Umineko's Battler (above), who is similarly tsundere towards witches and magic.
In Black Butler Ciel makes a contract with a demon, promising his soul to said demon. He is not unaware of this fact. Yet, in the anime version, somewhere between dealings with soul collecting Shinigami and psycho fallen angels, he, while siting next the demon he sold his soul to, claims that he doesn't believe in souls. (This is not true in the manga.)
In Naruto, Tsunade states the ghouls and ghosts are "just a bunch of hooey". But she's saying it to the guy with a demon spirit sealed inside him. Also, Tsunade's grand-uncle and one of her ex-teammates know resurrection jutsu. And her two immediate predecessors as Hokage each knew how to summon a Shinigami. And her dead boyfriend had invented a jutsu to temporarily transform himself into something akin to a ghost. To be fair, this is only seen in the Filler, which can be rather bad, particularly the later episodes.
Pokémon now has Dent/Cilan, who seems to come up with every "logical" explanation he can think of for supernatural events, such as an object floating through glass, EXCEPT that a Pokemon might be using Psychic.
In Ghost Sweeper Mikami, the protagonist is called in to help with a possessed patient of a Western-trained doctor. The doctor claims he cannot determine a cause of sickness, which is incredulous taking into account the levitation, horror face and swirling ghost energy around the victim. Doc responds by rolling around on the floor loudly denying the existence of the supernatural in a "La la la I can't hear you" fashion. He gets better by the end after encountering the possessing spirit and personally aiding in the fight with what he learned in medical school... A flying drop kick from his amateur wrestling team days! After acknowledging that the supernatural exists, he vows to prepare for any future occurrences... By training in his wrestling again.
Played for Laughs in Makai Ouji where it's first exaggerated and then subverted with the protagonist William, who takes a ridiculously long time to accept that demons are real despite having witnessed numerous inexplicable phenomena and the fact that two of them follow him around all the time.
InuYasha: Bankotsu of the Band of Seven explicitly tells Kikyo that he doesn't believe in an afterlife, despite the fact that he lives in a world where youkai and magic are general knowledge, as well as the fact that he's an undead human talking to another undead human who has to absorb souls to survive.
The modern Mr. Terrific in the Justice Society of America is an atheist, and he was questioned about this and gave the example mentioned (that there were godlike, or close enough entities running around who didn't call themselves gods). Sometimes he has excellent reasons for his beliefs and sometimes he doesn't, Depending on the Writer. Some writers like to use him as a Strawman Atheist.
Doctor Terrance Thirteen, the Ghost Breaker, is The DCU's preeminent example, earnestly believing that aliens (like Superman), magicians (like Doctor Fate) and supernatural beings (like The Spectre) simply don't exist at all. He's treated unilaterally as a joke. Ironically, in his original appearances before continuity held sway (that is, before The DCU was firmly established as a Shared Universe where nearly all DC properties resided), the ghosts and magicians he went up against always were fake and his skepticism was presented as a virtuous trait; but when continuity started drawing all DC books into one reality, he was first shown the spirit of his dead father by the Spectre, then he was teamed with the very mystical Phantom Stranger, and from then on he was always wrong, simply because the Stranger's very existence demanded it be so. Dr. 13 currently lives outside of the time stream, aware of his own fictional nature; he is teamed with an alien, a vampire, a French caveman, and a talking vampire gorilla with Nazi leanings, his daughter is a rather powerful witch, and he believes none of this.
There have been two alternate takes on Dr. 13, making his skepticism something other than the Idiot Ball. In Neil Gaiman's The Books of Magic, the fact he doesn't believe in magic means it simply doesn't work around him, in a cross between Clap Your Hands If You Believe and Weirdness Censor. In Grant Morrison's Zatanna he visits a mystical dimension and is happy to admit something's happening, but defines it all in scientific terms. (Quantum mechanics and M-theory get a lot of crap past the scientific radar.) There's also the Architecture and Morality take, wherein he's simply strongly in denial of reality.
He's met the DC comic staff so he knows they're all fiction.
Dr. 13 frequently alternated in stories where the Phantom Stranger appeared opposite him showing a prior story that was pure trickery he'd revealed only to have things a bit more supernatural (obviously) much of but not always when they were together. He also once disproved that ghosts haunted a house by showing it was actually ALIENS using the house as a stopover point as they teleported across the universe. He's always been the example of the devout worshiper of science whose blind-spot always has him refusing to accept the evidence of supernatural things because he operates under the (obviously proven wrong) premise that nothing supernatural actually exists.
In the New 52The Phantom Stranger title, he's been reinvented as a "scientific occultist" in the mould of Egon Spengler. His ancestor, the original Terrence Thirteen in All-Star Western, on the other hand, is the ultimate Flat-Earth Atheist: at one point his ghost chides the modern-day Terry for believing in the supernatural.
In an issue of DC's Checkmate, a wizard describes magic to an atheist skeptic as "the cheat codes to the universe".
In an issue of Planetary, The Drummer uses almost the exact same explanation to Hand Wave magic into the realm of his infomancer powers.
In the Marvel Universe, Science Heroes like Iron Man and Hank Pym acknowledge that The Mighty Thormight be an actual god (though they tend to think of him and all other mythological beings as closer to sufficiently advanced aliens; Thor was actually retconned to be this by Warren Ellis, but who knows if it stuck) and that characters like Doctor Strange, The Beyonder, and the Scarlet Witch are doing something beyond their comprehension. That doesn't mean they're comfortable with not understanding what's going on, don't stop looking for ways to explain it, or that they're specifically religious. The closest we ever get is one or two incidents of straight-up desperation praying after all viable options have been exhausted. The only science hero that has no problem accepting all of this is Bruce Banner. Though this is a relatively recent development and there are several older stories where these guys have little problem accepting magic and gods, or at least being convinced of it rather quickly. Flanderization in action.
Quasar started out his series as an atheist/antitheist, but after the seminal "Cosmos In Collision" storyline a couple of years in, he became more of an agnostic ("Maybe I'm not the atheist I thought I was. Maybe I just haven't discovered the god that's right for me..."). This was likely helped by the fact that in said storyline, he died and was resurrected. God in the Marvel Universe is called The One-Above-All who appeared to the Fantastic Four as Jack Kirby, a person they know. It runs a bit in the family: at one point Quasar has a conversation with his by-then deceased father who is quick to point out that the fact the conversation is happening is still no proof of such a thing as an afterlife.
Touched on by the City of Heroes comic books. A sizable portion of the eponymous city has been overrun by zombies powered by the magics of ancient evil "gods", another group of mages summon ghosts and devils and gods regularly within city limits, and one of the major canon heroes makes his armor out of demons. Many heroes still scoff at the concept of Prometheus and Zeus when talking to the former is an important part of making the local phlebotinum work again.
The hero of The Savage Dragon remained an atheist even after being sent to Hell (by a villain's magic), witnessing a fistfight between God and Satan, and having a conversation with God. His rationale throughout the whole ordeal was that it was just some weird dream. Later storylines have involved Godworld, a planet housing every god of every pantheon, but these gods are treated like any other superpowered menace, with the question of their legitimacy being unimportant to the story.
Brainiac 5 of the Legion of Super-Heroes. In the postboot continuity he scoffs at his teammate Shikari's feelings about finding a way home during the "Legion Lost" storyline. (In his defense, though, the setting he lives in is at the "sufficiently advanced technology" stage or close to it.) If anything, the end of that arc justifies Brainiac 5's skepticism, as the creator deity worshiped by all the local lifeforms turns out to be a Sufficiently Advanced Alien and former teammate Element Lad.
The snarky Loveable Rogue drow elf Downer from Kyle Stanley Hunter's comics Downer: Wandering Monster and Downer: Fool's Errand calls himself an atheist, despite the fact that he lives in a Dungeons & Dragons world rife with magic and deities. This leads to problems, as no normal cleric will heal his injuries or resurrect him when he dies. Ironically, in the end it was Downer himself who ascended to become the God of the Game (for about five minutes) when the Ulolok channeled its power through a slain Downer.
In the Age Of Ultron tie-in for Fantastic Four, Mr. Fantastic tells sums up his views on afterlife thus: "I am a man of science. There is no God. There is no Heaven. There is no Hell." Just to put this in perspective, not only does he personally know Thor and Hercules, but he's actually met the Christian God as well.
He also was established as believing in God many times in the past.
Bill: I am alone. I look at the heavens and think them empty. And if not empty, I find the idea of worshiping whatever dwells there obscene. It doesn't change what is right. If there is nothing but what we make in this world, brothers... let us make it good.
Bill has never outright dismissed or challenged Thor's claims to godhood and made this statement after witnessing the damage of religious wars. His people were destroyed over the struggle between the traditional religions and the new belief of Bill as a god, the Skrull invasion of Earth in the name of their god, a madman causing genocide in the name of his religion, and further Skrull infighting over whether to follow the traditional Skrull gods or take Bill as their new god.
The X-Men were once sent to a world shaped according to Dante's Inferno. Colossus claimed he was proud to be an atheist when he saw how cruel God was. Nobody pointed this out.
Achille Talon has a guy claiming he isn't afraid of ghost because he talks with his revenant cousin at every full moon, and he is a skeptic. Actually the guy was part of the fake ghost conspiracy, but still...
Nicely justified in Neil Gaiman's take on The Eternals, when Mark Curry refuses to believe Ikarus is an ancient immortal who was worshiped as a god because he lives in the Marvel Universe. "It's a weird world out there, dude. But if Spider-Man said he got his powers from reading Chariots Of The Gods, guess I'd figure he was crazy too."
This is essentially the whole point of SHOOT First. The agents of the Secular Humanist Occult Obliteration Taskforce are atheistic as a rule, despite fighting supernatural forces from various religions. SHOOT considers such entities "Outside Actors" and characterizes them as powerful aliens or somesuch (more "not what they claim" than "not real") — and furthermore holds that buying into the idea that, say, the giant rock guy with writing on his chest is a golem, gives him greater power. At various points, many of the characters wonder if they're actually "right"; while the Outside Actors that they encounter seem pretty villainous, SHOOT has no real proof that their interpretation of their actions or their existence is at all accurate. One member actually secretly secured a document from the Vatican ensuring his passage into Heaven, just in case. He claims there's no doubt in his mind that his position is the right one, but that from a scientific standpoint it would be idiotic to not have a Plan B.
Another character has been trying to avoid her son's questions about what happens after you die, even though his father was a fire-breathing demon with horns and wings and the kid may be the Antichrist.
This trope is parodied in one part of a MAD article, "What if God Were One of Us?" In one of the gags, Woody Allen is having lunch with God in a restaurant (where God is eating spaghetti); Allen tells Him, "I want you to know I'm still an agnostic, even though you're right here in front of me, because it's hard to believe the omnipotence of a man with crab meat in his beard."
In Eugenesis Nightbeat angrily decries the existence of Primus, despite having seen him and been teleported across the universe by him, before taking part in a battle against Unicron, his religion's devil. Of course, he did watch Primus get killed a short time later as well. And as later events in the story prove, he might have a reason to doubt Primus after all...
Not quite atheism, but in Erik the Viking Harald the Missionary, who accompanies the Vikings on their quest, staunchly refuses to believe in the Norse gods and their mythology... even when they're standing outside the gates of Valhalla. He can't see it, because he doesn't believe in it (he is a Christian, after all), but it certainly causes a great deal of frustration with his crewmates. Turns out to be a plot device when the Missionary is the only one who can leave Valhalla to save them all, since he doesn't believe in it.
In a somewhat fridge logical example, Han Solo from Star Wars. At the start of A New Hope he doesn't believe in The Force, despite the fact that the Jedi were a major power in the galaxy up until about 19 years ago.
Han: It's all a lot of simple tricks and nonsense.
To be fair, even before the fall the Jedi were such a negligible percent of the entire population that most inhabitants of the galaxy had never seen one. Of course, because the galaxy loves irony, Han ends up married to a Jedi, with a Jedi brother-in-law, and three Jedi children.
In Tim Burton's Batman (1989) it takes a great many characters quite a while to acknowledge that Batman might exist, and even then they're not willing to say so publicly. Alexander Knox (the only halfway-credible person who believes in Batman from the beginning) points out early on that, for the past month, there has been at least one sighting of Batman every week. But Harvey Dent dismisses the stories of Batman sightings as tales of "ghosts and goblins," and Eckhardt the police lieutenant insists that the slum dwellers who claim to have seen a bat-creature are "drinkin' Drano." Vicki Vale does pretend to believe, but this is only to convince Knox to join her in an official investigation of the sightings, which Vale hopes will advance her career and maybe even win her a Pulitzer Prize. Commissioner Gordon is the second major character to catch a glimpse of Batman...but he'd rather just sweep the truth under the rug, partly because it would embarrass Gotham City's police and partly because, since Batman was directly responsible for Jack Napier's near-death when the police needed Napier alive as a mob informant, Gordon frankly would rather believe that Batman does not exist.
In The Coffin Joe Trilogy, the title character refuses in to believe in God, Satan, and general supernatural activity, despite frequently being a target of ghostly/demoniac apparitions within the trilogy. It's never confirmed if the apparitions are real or a product of his mind.
In Jesus Christ Vampire Hunter, the title character gets attacked by a mob of atheists. "You don't know us, because we've never talked to you before!" Yeah, it's a weird movie.
Walter Peck in the first movie firmly refuses to believe in ghosts even when his own actions cause the rampaging ghost menace in the first place (or maybe he had his denial blinders on). Plus the hundreds of eyewitnesses who have seen ghosts and seen the Ghostbusters at work. Peck's accusation that the Ghostbusters use gas to cause hallucinations is made without the slightest shred of evidence.
In the B-MovieVoyage to the Planet of Prehistoric Women, the eponymous women come to accept that their various nature gods are false after they fail to kill the human astronauts. At the end, they declare the humans' dead robot to be their new god. This ignores the fact that their prayers to the gods, although failing to kill the humans, did cause volcanic eruptions and floods, and killed the robot that they accept as the "strongest god".
Referenced in Dogma when Loki, the former Angel of Death, talks to a Nun early and claims to have become an atheist due to a bizarre interpretation of Lewis Carroll's poem The Walrus and the Carpenter, which convinces her somehow to give up organized religion. His friend Bartleby points out that he knows for a fact there is a God, that Loki has stood in His presence, and He has spoken to Loki personally, yet Loki just claimed to be an atheist. Loki replies he just likes fucking with the clergy.
Frequently parodied in Discworld, where atheists are often hit with lightning on clear and sunny days. Feet of Clay features Dorfl, a golem who will only believe in gods when they can be proven by rational debate. Offler decides to settle this by hitting him with a lightning bolt but Dorfl simply shrugs this off, saying, "I Don't Call That Much Of An Argument". It seems that Dorfl is the gods' worst nightmare — a ceramic atheist. Fireproof!
In Small Gods, a bartender in an Ephebian bar for philosophers says: "We get that in here some nights, when someone's had a few. Cosmic speculation about whether gods really exist. Next thing, there's a bolt of lightning through the roof with a note wrapped round it saying 'Yes, we do' and a pair of sandals with smoke coming out. That sort of thing, it takes all the interest out of metaphysical speculation."
Which is why the Library of Ephebe is roofed in copper.
The gods also aren't very fond of being fooled with. A footnote in Hogfather describes one philosopher indulging in the Discworld equivalent of Pascal's Wager... only to wake up in the afterlife surrounded by a lot of deities with pointed sticks saying, "We're going to show you what we think of Mr. Clever Dick in these parts."
Sergeant Simony in Small Gods, who tells the manifested god Om, "Don't think you can get round me by existing!" Interestingly, Om doesn't actually mind this, and notes that, as the reason gods want worshipers is because Gods Need Prayer Badly, such fervent belief in nonexistence works just as well, so an atheist that enthusiastic is actually worth more to a god than a casual churchgoer.
Played with in the opposite direction with Mightily Oats from Carpe Jugulum, an Omnian reverend who has a crisis of faith throughout the story. Granny Weatherwax helps snap him out of it by telling him that if she saw her god personally save one of his greatest disciples in front of a large crowd, she'd live her life defending her religion to the bitter end.
Granny's standard approach to gods is that just because they exist is no reason to go around worshiping them - it only makes them start putting on airs.
Whether Reg Shoe believes in the existence of the gods is uncertain, but in Jingo he takes a very rational approach to what his Token Religious Teammate Visit-The-Infidel-With-Explanatory-Pamphlets is claiming as a miracle. This in spite of his being a zombie and, moreover, being a watchman in Ankh-Morpork, where he's seen the strange things that go on all the time. To be fair, one of the things Visit claimed was "a miraculous rain of rain"
Also, Uncle Andrew, who refused to believe that the animals were talking and trapped himself in a Weirdness Censor.
And then there's Eustace in The Voyage of the Dawn Treader. He refuses to believe that Narnia isn't on Earth, while on a ship whose X.O. is a three-feet-tall talking mouse. The movie throws in a minotaur as the Master at Arms to make this even more ridiculous. The inclusion of the minotaur is made even funnier when he and a human shipmate make fun of Eustace for talking to a seagull and expecting it to respond, with their implication that Eustace ought to have known better.
Prince Rabadash is a variation - although he believes in the Calormene Gods, he also believes that the ending of the White Witch's eternal winter has come about through "the alteration of the stars and the operation of natural causes." Despite the fact that the Calormenes have been entertaining fauns, talking animals, they know that Narnia is guarded by "a demon...in the shape of a lion" and that the long winter was caused by a witch.
Richard from The Sword of Truth series denounces the concept of an afterlife where people are rewarded or punished for their actions, because "nobody has ever come back from the grave to describe conditions in the next life." This despite having personally conversed with the spirits of the dead at least three times, and having gone to the underworld and come back.
In David Eddings' The Elenium, the Elene people believe in only one God and their religion is almost exactly like the Catholic Church. Their God doesn't respond directly to them and they never see him. However, they do live on a planet with about 1,000 other gods. What is really weird is when the Church Knights (the military arm of the Church) need magic to fight magic, they get four priests from four of the other gods (who, again, the Church says don't exist) to teach them magic. And that magic is praying to the other gods (who according to them don't exist) for spells. Other races of people do find the Elene religion strange that way, especially the ones who actually meet their gods. Amazingly enough, Eddings gets it to work. The Elene god, in fact, is even okay with this. He and the Styric pantheon have a deal worked out.
Thomas Covenant the Unbeliever from The Chronicles of Thomas Covenant is a good example of the subtrope of the atheist dropped into a supernatural world. It takes him the whole first trilogy to accept that The Land isn't just a figment of his imagination. Even then, he doesn't stop believing the Land is a hallucination. He just concludes that it's an important hallucination.
The Left Behind series. After a wide variety of miracles, divine intervention, etc. it began to strain disbelief that so few people would convert.
Early in Perdido Street Station, Isaac (a "scientist") expresses just such sentiments. However, given that his world includes sentient steam-powered robots, Lovecraftian horrors, aliens, electricity, alchemy, necromancy, parallel universes, and a few other strange forces, gods might be the only thing it's safe to disbelieve in (though there's plenty of religions available).
In Stephen King's novella The Mist, the main character refers to a group of "rationalists" who refuse to accept that something very strange and dangerous is happening out in the eponymous mist as "The Flat Earth Society." I don't think the term comes up in the movie, though. note Believe it or not, the Flat Earth Society is a Real Life group of modern day people who believe that the Earth is in fact flat.
The gods themselves seem more like ineffectual echoes than genuine powers of the universe, so disbelieving them can be seen more as disbelief in their hype of themselves, rather than in their subjective existence (all observations of gods in the book is subjective — no omnipotent narrator's solution is presented).
"Why do they want gods? We need people. That is what I believe. Without other people, we are nothing."
The Tolnedrans in The Belgariad worship a God that loves money, which sent them down a road to love money more than Gods, so that they're effectively atheist businessmen, and their God couldn't be happier with them. Most Tolnedran characters will cling to their atheism no matter how much the world's supernatural elements prod at them, including a scene where General Varana spends a tactical meeting facing away from the other commanders so that he won't have to see the sorcerers he's working with shapeshifting and casting spells.
Further proof of this trope by the Tolnedren's, according to any Tolnedran, and the entire Tolnedran government, there is no such thing as magic, yet there are also specific laws making it illegal to use the very magic the law makers agree does not exist.
Sanya's attitude about the whole thing is that it doesn't matter if his power came from God or not, he's helping people who need it, and that's all that matters. Or he's just insane. He's in no hurry to figure out which explanation is true.
Dresden himself, despite being best friends with another sword-bearer, and having had open discussions with Archangels, doesn't consider himself a "Believer", either. This is less a lack or weak belief, but more of a difference of opinion about a certain Deity's Modus Operandi.
Despite being a Nay-Theist himself, Dresden finds Sanya's agnostic views extremely amusing when he first hears them. He is quick to point out all the supernatural things Sanya deals with on a regular basis, and ask if a Knight of the Cross is even allowed to be an agnostic.
The Mi-Go, H.P. Lovecraft's Fungi from Yuggoth, appear to be a race of these, at least according to some Cthulhu Mythos materials. Though they live in a world overflowing with monstrous, supernatural beings with horrific powers, rather than worshiping them as gods like most mortals aware of their existence, they plan to use their science to either control or destroy these entities. In contrast to the hopelessness that surrounds any human confrontation with the Mythos' various horrifying creatures, you get the feeling that the Mi-Go might just have some chance of pulling it off, probably because, unlike humans, their science is not inhibited by old-fashioned limitations like ethics. When you think about it, they may just be the scariest damn things in the entire Mythos.
Alternatively, they may just have Outgrown Such Silly Superstitions. After all, many if not all of the 'supernatural' entities of Lovecraft's creation are themselves 'only' alien lifeforms that humans — and insane cultists in particular — simply easily mistake for gods or demons.
According to The Whisper in Darkness where the Mi-Go are introduced, they do seem to worship Shub-Niggurath and Nyarlathotep. It does sound like a pragmatic relationship, though; you really don't want to annoy forces like that, no matter how great your civilization is.
The Whisper: To Nyarlathotep, Mighty Messenger, must all things be told.
Jayce in the Mortal Instruments series considers himself an agnostic even though he belongs to an order founded by angel and has met and killed many a demon himself. He claims it's because he's never personally met an angel or knows anyone who has but he does know that holy water, sacred ground and blessed weapons work because he uses them on a regular basis!
Jalil in the Everworld books is a teen-aged atheist from this world sucked into a world where various mythological deities are real. He's fairly smart about it, but more-or-less claims them to be Sufficiently Advanced Aliens and/or that the laws of physics in this world are just different and assumed to be "magic".
Interestingly, this series plays with the trope with another character: April, a devout Christian brought to Everworld. While she seems more open to displays of the obviously supernatural, she also claims the various deities aren't "real gods" while at the same time having a small crisis of faith.
Jalil's issues are further examined by the other characters' opinions. The acid-tongued, magic-loving Senna in particular has a few interesting things to say about it. "No wonder you don't believe in God or gods: Thou shalt have no other gods before Jalil."
In Saturn's Children by Charles Stross, all the characters are robots (though that word is considered obscene). Most of them, based on design schematics and such, believe that they were created by human beings. A few, however, believe in the holy doctrine of Evolution, and its prophets Darwin, Dawkins, and Gould.
In Warbreaker, Lightsong is a god who doesn't believe in his own religion. He has an epiphany towards the end. Another character, Siri, is married to the God King but doesn't believe in him. In both cases, though, they believe in the existence of the potential deities, just not their divinity. Siri does believe in 'a' god, just not the one she's married to.
In Towing Jehovah by James Morrow, God Is Dead and his two-mile corpse is floating in the Atlantic Ocean. The Vatican hires a disgraced oil tanker captain to tow God's body to the Arctic where it can be kept on ice before it rots away or is devoured by sharks. One of their primary antagonists is the Central Park West Enlightenment League, who upon hearing the news, try to destroy the corpse with bombs to remove concrete evidence of a deity. One of their members does remark if they were truly committed to scientific reasoning they should try to study the corpse and accept the possibility they'd been wrong all along, but the majority reject her.
Given how vastly the notion of God physically floating dead somewhere reduces His stature, you'd think it would be the Vatican not accepting and indeed trying to destroy the evidence.
Given that the Vatican was commanded by the Heavenly Host to give God a proper burial in an ice cairn, I think their options were rather limited.
In Caitlin R. Kernan's novels, the characters spend a suspicious amount of time fervently denying anything supernatural is happening... including when they're blasting ghouls into chunky salsa with shotguns. Former psychic detective Deacon Silvey is a repeat offender.
In the Kitty Norville series, the masquerade was broken in the first book of the series. Kitty's House of Horrors is the seventh book, set about four years after the start of the series, and is probably the first time the reader meets a person who doubts the existence of the supernatural. Author Conrad Garrett argues that people who claim to have supernatural powers are frauds or crazy, that video footage of a werewolf shapeshifting is CGI, and that CDC reports on were-people and vampires are the result of collusion with drug companies who want to make money off the conditions. He only changes his mind when he sees Kitty shapeshift.
Lampshaded in some of Patricia Briggs' Mercy Thompson novels. Werewolves have recently gone public; the fae have been officially out for a decade or so, and demons are also real, but the protagonist meets quite a few people who don't believe in vampires or ghosts, and her friend Adam, a werewolf, doesn't believe in God (although she does herself).
In Christopher Stasheff's Her Majesty's Wizard, an agnostic from Earth is transported to another world where he discovers not only his magical powers, but the unequivocal Judeo-Christian deity (God) and opponent (Satan) who directly and consistently interfere in human affairs. Priestly blessings have direct and easily detectable effects, the hero interacts directly with his personal devil who tries to drag him into hell, he runs into at least one saint who tells him what to do after transporting him from a wrecked church into a fully restored one and back again, the act of being knighted by a king (who rules by divine right, and who happens to be mostly dead at the time) actually confers martial abilities, and at the end after the chief bad guy is defeated we see hordes of devils stream out of the sky and compete for his soul, only being banished by the intervention of priests. Stasheff pointed out in the afterword that medieval people saw God and the Devil everywhere in their daily lives, and this book is an attempt to show that where most fiction of this type completely ignores this aspect of their lives.
In S. M. Stirling's Emberverse, a universe that's kicked off when a bright light rends inoperable all modern technology at once, The Chessmaster Sandra Arminger remains one of the few atheists. She admits that the evidence in favor of religion and magic in her universe makes this an illogical position, and says that she has attempted to pray. Her prayers have been ineffective, however, because in her heart she does not believe.
Juniper: You believe in nothing, you pray to nothing, and you are answered by — nothing!
Sandra(wryly): Is nothing sacred?
In Piers Anthony's Incarnations of Immortality series, one's spiritual beliefs, among other factors, determine what kind of afterlife one experiences. Consequently atheists, who don't want to go on after death, despite living in a world of magic as well as science, have souls that end up disintegrating upon their deaths.
In the setting of Philip K. Dick's A Maze of Death God is openly real, and prayers are a commonly accepted way of solving problems, though they usually have to be carefully composed and transmitted by radio into outer space in order to work. Dr. Babble, however, is an atheist who believes that the "God" in question is just a Sufficiently Advanced Alien.
The characters in the Knight and Rogue Series are fully aware that there are two gods out there who somewhat violently protect plants and animals, but as no greater being guards humans there's no serious religious practices.
In the Warrior Cats series, there are two. Cloudtail refuses to believe that StarClan exists, despite seeing his leader come back to life after being killed and the fatal wounds healing themselves. But even more notable is Mothwing, a medicine cat. She had a prophetic dream herself right after being apprenticed, and everything that Leafpool has told her, which she couldn't possibly have known on her own, happens to be true. She has also seen her own leader lose lives and come back to life. As part of a medicine cat's job is to be the spiritual leader of the Clan, this makes her the equivalent of an atheist priest.
She later starts training a religious apprentice, Willowshine, who knows that Mothwing's an atheist and interprets mystical dreams and omens for her. Mothwing did originally believe in StarClan and see them, but her brother (an evil, manipulative bastard) convinced her that they weren't, and after he dies, she can't quite bring herself to trust in them again. Essentially, she wants to believe in StarClan, but she can't risk getting her hopes dashed again.
And in the fourth series, Mothwing's disbelief is finally broken, (according to the author) when the feline equivalent of Heaven and Hell take physical forms on Earth to battle against each other. That's what it took.
And earlier in said fourth series, after seeing something that was clearly an omen by cat standards (a burning reed that wasn't extinguished, even by constant rainfall over it) she brought another medicine cat over to see it, saying that she didn't believe it was a sign, but she knew that he would and that it might be important. One imagines that she was just in denial to begin with.
Elizabeth Bathory in Count and Countess. She and Vlad Tepes can write letters to one another despite living in two different time periods, but she still doesn't believe in the existence of a deity.
Dunk, the hero of the Blood Bowl novel Rumble in the Jungle. In that book he encounters his long lost sister who is haunted by the ghost of their late mother. Dunk is unshakably convinced that the ghost isn't a real ghost at all but merely a daemon who (somehow) gained the shape and memories of their mother despite no particular evidence such a thing is possible and his own frequent encounters with more physical undead like vampires.
The Bible: The parable of the rich man and Lazarus in Luke 16 presents unbelievers this way, as people who won't convert even if they witness miracles.
If they do not listen to Moses and the Prophets, they will not be convinced even if someone rises from the dead.
Though the terms "unbelievers" and "atheist" had broader meanings back in the day, and referred to Nay Theists and people who might believe God (or gods) existed, but did not have faith in Him / them.
Doubting Thomas. After all the miracles he'd seen Jesus perform (including raising a man from the dead), and despite being willing to accept his divinity, and despite Jesus prophesying that he would return from the dead, Thomas still didn't believe he'd done so until he saw it with his own eyes. An admirable spirit of skepticism, perhaps, but not doing a very good job as an Apostle.
Chanters of Tremaris has a non-deity version of this trope in the character of Trout, who refuses to believe in the existence of magic, even after he's seen it used. It later turns out to be a Justified Trope, as the spell in question was a very, very high-pitched spell of illusion, and Trout is deaf to high noises which rendered him immune to its effects. After further exposure to magic that he can see and hear, he gets over it.
Harry Turtledove's Videssos Cycle has Marcus Aemilius Scaurus who doesn't believe in the opposing Scotos and Phos, despite all evidence, until one of them practically bites him on the ankle.
In Dangerous Spirits, Meg maintains her position on the reality (or lack thereof) of Sol and Alexei's spiritual encounters, even after witnessing it first-hand.
In Gifts by Ursula K. Le Guin, Orrec's mother Melle has a difficult time fitting the magical powers of the domains into her lowlander, anti-magic worldview. The people of Caspromant try not to use their gift of unmaking for her comfort.
In John Ringo's 'Queen of Wands', all of the deities and devils in all religions exist and interact with human beings, with "The White God" (the Judeo-Christian Trinity, directly from the Christian Bible, Old Testament in this case) being the most powerful but still only one of the gods. The main driver of one of the stories in that book is that an "Old One" is summoned, and is well on its way to destroying the USA. During a conference call with government officials who are deciding how to deal with the Old One, the White God personally speaks through his representative, the main character and lays down the law. And even then, multiple people in the government still don't believe in deities, and/or refuse to accept their divinity, and refuse to support any actions which might violate the principal of separation of church and state, such as having the President go on television to pray for deliverance from the Old One (who at this point has been shown to be immune to nuclear weapons). Their insistence on not believing, in the face of unequivocal evidence to the contrary, is this trope.
His friend Lyta Alexander tells him that when a telepath is scanning the mind of a person who dies, he or she can see the person's soul going through a portal to the beyond, although she acknowledges that it may just be the only way the brain can interpret what is happening.
And the Minbari broke off the war with the Earth Alliance because they found "undeniable proof" of Minbari souls being reincarnated in humans, namely Sinclair and other pilots they captured. Apparently they have technology that can scan and identify souls. Except it's later revealed that it didn't detect souls, but Sinclair/Valen's DNA.
Star Trek: Deep Space Nine also offers many classic examples, specifically in regard to the Bajoran Religion. Despite the existence of bona-fide holy relics in the form of the Orbs of the Prophets and the sworn statements of several high-ranking Starfleet officers, the Federation still treats the Bajoran Religion as little more than fairy tales. Prophecies and visions of the future are almost always dismissed as hallucinations and wild speculation, despite the well known fact that the incredibly powerful beings known as "the Prophets" exist in a state outside of time and are perfectly capable of giving visions and inspiring prophecies. That's still more along the lines of the TrekNo Such Thing as Space Jesus staple than this, though. A few officers at least come around to the idea that the "wormhole aliens" are definitely powerful beings that have a relationship with Bajor, but worshipping them is exlusively the province of Bajorans themselves.
DS9 actually spends a lot of time playing with this trope, with both the Prophets and the Founders worshipped as Gods by some groups while others view them as simply non-humanoid aliens with advanced knowledge. The question the show never quite spells out is "what makes a god?" The Founders, despite their legitimate claim to Physical Godhood, are portrayed as just arrogant genetic-engineers (albeit engineers capable of uplifting or even creating entire sentient species). The Prophets, on the other hand, are left more ambiguous in the veracity of their divinity (ultimately a matter of faith): it's granted that they are essentially omniscient, but the matter of their intentions (benevolent or ambivalent) and their power over the physical (or spiritual) world can be unclear.
The show also gets a lot of dramatic mileage out of Sisko being the Messiah of a religion he doesn't believe in.
Torchwood's Jack Harkness is a possible example. The finale of the first series opens with him scoffing while another character reads from The Bible. By the end of the episode, he's fought a monster named Abaddon. Whether or not a lot of the characters are supernatural, though, is ambiguous. Justified in that at this point Jack has died and come back to life several hundred times and does not consider the resulting experiences consistent with the existence of God. He's also been consistently searching for proof of something after death, but all he's gotten from people who've been there is, "None, I got nuthin'."
In the 1998 Merlin series, King Vortigern does not believe in magic, or in The Fair Folk, or in the gods of Celtic Mythology, or in the Christian God. This is despite witnessing magic, meeting Queen Mab, a Fay Goddess, and dealing with the wizard Merlin and hearing some of his (eventually proven correct) prophecies. Vortigern does accept help from Mab to thwart Merlin and recognizes her powers. It's not so much that Vortigern doesn't believe; he simply doesn't give a shit.
Both Cavil and Adama present themselves as atheists in Battlestar Galactica, long after it seems that either souls, gods or super-human / super-Cylon beings almost have to exist.
In a non-fantasy version of this trope, United States Of Tara features Bryce Crane, one of Tara's multiple personalities who doesn't believe in DID.
While Agent Scully in The X-Files is an example of, well, an Agent Scully, Mulder qualifies on notable occasions. He is more than happy to believe in Yetis, Psychics, Vampires and Little Green Men, but any hint of an Omnipotent God in the equation and he suddenly becomes more skeptical than Scully at her most ardent. Which makes quite a bit of sense if you consider that he does not need an omnipotent god to explain anything strange until such a being is necessarily part of the occurrence. Scully herself, a Catholic, reverses roles with him on any occasion when the phenomena is religious (nearly always Christian) in nature, immediately shedding any skepticism.
Inverted in Stargate SG-1. Many worshipers of the Goa'uld and Ori see SG-1 as this. When the heroes try to explain that the "gods" they worship are in fact Sufficiently Advanced Aliens, a frequent response is "what's the difference?" This is particularly true with the Ori, given that they are ageless beings without physical form who gain power from being worshiped. Or at least they were, before the heroes killed them.
The show Supernatural is much like The X-Files in how it features Flat Earth Athiesm. Dean is the primary example. While he very easily believes in the supernatural (hence the name of the show) and Hell, he simply flat-out refuses to believe in things like angels, Heaven, and God. "Gods" are simply very powerful monsters, but you can still "gank" them. Dean is forced to face his lack of belief after he returns from Hell, when faced with the angel Castiel. Cas becomes a regular on the show, as does their "prophet" Chuck who is later implied to actually be God.. Even the demons (re Lucifer, who is actually a Fallen Angel) end up stressing the fact that God exists—He might not be there, but He does exist. Lucifer goes on this long-winded schpiel about his devotion to his Father (God) being the reason for his falling from Heaven (though its more or less stated that he was really just jealous that God seemed to love humans as much as he loved angels). Dean, while eventually admitting to the fact that God exists, never fails to ruffle the feathers of all the angels he comes across, simply for the fact that they are, as he puts it, "dicks" (though nearly all of the Jerkass angels seem to believe God Is Dead, or at least has abandoned everyone This is where at least 60% of the humor from season 5 onward comes from, still managing to question the core accuracy of the Bible (although they quote the Bible for things it doesn't actually say), or just religion in general.
Jack in LOST is set up early on as the "man of science" who refuses to believe anything weird is going on with the island for far, far longer than any reasonable person. The worst of it is when he flatly denies seeing the island disappear right in front of him.
A truly bizarre variant in Bleak Expectations, where Harry Biscuit claims to be an Agnostic desite having just fought an army of demons from Hell itself. It gets even more bizarre later on, when we find out God exists. And He is Harry Biscuit.
The Professor in Old Harry's Game vehemently denies the existence of God, despite being in Hell.
The atheist philosopher Oolon Coluphid in The Hitchhiker's Guide to the Galaxy is a variation. One of his antitheistic books, "Well, That Just About Wraps It Up For God", is said by the Guide to hinge entirely on the argument that God refuses to prove that he exists, for proof denies faith, and without it, he is nothing - but he did prove that he existed as the Babel Fish is a creature far too useful not to be intelligently designed, and therefore God cannot exist as he has proven his own existence. The Guide acknowledges that this argument is 'a bunch of dingo's kidneys'. The book version of the story expands on the theism of the setting, where God does definitely exist and even left a final message to humanity. Unfortunately, God Is Inept as well.
In Hamlet, the title character gives a speech in which he calls death "The undiscovered country from whose bourn / No traveler returns" in spite of the fact that he's spoken with the ghost of his father.
In the Forgotten Realms, there are still atheists. This is despite the fact that gods regularly take physical forms and rampage around the countryside, and that new gods rise while others die in every decade. Really, the existence of gods would be no more questionable than that of President Obama... Incidentally, there's a Fate Worse than Death reserved for Atheists (and those who, ironically, decide to worship the Overgod Ao).
Or if they believe in the existence of the gods in general but doesn't choose a specific patron deity. Or their patron deity happens to be dead. Or if this patron deity rejects the worshiper for whatever reason. The fate in question: One's soul is strapped to the Wall of the Faithless and slowly digested by it over the course of millennia.
In the new edition, a continent as well as two countries has been brought over from a world where gods haven't existed for about 30,000 years, so anyone from there might have a justification.
Yet another reasoning behind it is the old Athar standby of agreeing that there does indeed exist powerful planar beings called gods that are worshipped by many — but that doesn't make them proper gods. Considering that (up until 4th Edition) several gods had died within human living memory, you can see where they're coming from.
In the backstory of the setting, the empire of Netheril ultimately fell (and magic across the Realms was diminished from what it once used to be) because its wizard-rulers convinced themselves that the "gods" were really just other wizards who knew tricks they didn't feel like sharing. Eventually, one wizard called Karsus did come up with a spell designed to let him attain godhood, and from a certain point of view could be said to have succeeded in casting it, too...but he couldn't handle the sheer power that came with his "success", and that's why there is no deity called Karsus in the Faerunian pantheon today and how the title of the Realms' goddess of magic changed hands from Mystryl (who performed a heroic sacrifice to save the world) to the first Mystra.
In The World of Greyhawk, Oerth, the native clergy of the Flanaess is opposed by the so-called Skeptics movement established primarily in the County and Duchy of Urnst. The more extreme members of the movement believe that the gods of Oerth are pure fiction and that their clerics are frauds, with clerical magic not granted by divine sources but coming from within like arcane magic or psionics. The more moderate Skeptics admit the existence of beings called gods, but they claim that these gods did not actually create Oerth and furthermore many of them started out as mortals who ascended to demigod status and later to godhood. Therefore the Skeptics deny these gods their faith. They're little more than a fringe group, and the one time a Skeptic gained political power, it turned out to be a disaster—one of the previous Dukes of Urnst drastically raised church taxes when he took the throne, caused a series of riots in the nation's capital, and ended up dying when no cleric would heal him after he was wounded in battle with mountain raiders.
Since Planescape is a Clap Your Hands If You Believe setting, this is common; although the Athar tend to be more Nay-Theist than this, there are others who are not. (The fact that the Powers, while existing, aren't necessarily the prime movers and shakers of the setting helps.) There is also an adventure involving killing a god by inducing Flat Earth Atheism: A Mind-Control Device that you could use to give a suggestion to the entire population of a prime-material plane that their God did not exist... Which would make that belief come true.
In Ravenloft, atheism is common in Lamordia, a domain where mad-scientist-style skepticism prevails. In other domains, heretical philosophers sometimes speculate that divine magic is actually derived from the Dark Powers, rather than the gods it's commonly attributed to; however, as most ordinary people have never even heard of the DPs, theirs remains a minority opinion. (Out of character, it's left up to the DM to choose.)
In fact, this was why Dr. Mordenheim was damned and cursed in the first place. He refused to believe in any power greater than man, being an admitted atheist all his life. However, the gods did exist, and they saw his attempts to create life using technology as blasphemies. To punish him, they granted his wish, breathing life into his creation, cursing him with something that would condemn him forever for the evil he was bringing into the world. While Adam, his creation, is the true darklord of Lamordia, Mordenheim is as much a prisoner of the Ironic Hell as Adam is.
In a metagame example, a minority of Ravenloft game masters opt to assume that there are no "Dark Powers" in their individual campaigns, and phenomena such as the Mists, curses and Powers checks are simply a byproduct of innate metaphysical laws that operate within the setting.
The Eberron setting avoids this trope. Divine Magic is the product of faith, Arcane Magic is just a force of the world. Someone with the proper training could have divine magic if he believed enough. It's even possible for clerics to turn from their religion and keep their spells. In fact, some mortals (and undead) have set up faiths centered around them, and their clerics get divine magic. Gods do not take physical form (except for one, The Traveler, and it's more the stuff of myth, like in ancient Greece). There are miracles which could be the work of the gods, but that is open to interpretation. In the setting, the actual existence of gods is up to a character's belief, as the gods do not act as proactively as they do in the Forgotten Realms, for example. Fiends are the original occupants of the material plane, and their religious implications are downplayed. Angels and Devils are just Outsiders. There are even some books that suggest the gods are based on the legends of certain Dragons.
One AD&D sourcebook reveals that Asmodeus feeds on the souls of atheists. The book acknowledged that this is difficult in a setting where Gods are manifestly real. The tactic of Asmodeus is to grant magical powers to someone, allow a cult to grow, and then withdraw those powers. The cultists become disillusioned and believe their leader a charlatan, at which point they are "vulnerable" to atheism.
In Warhammer 40,000, the Emperor of Mankind wanted to eliminate all religious beliefs from the Imperium and make mankind trust in science and logic. However, it's heavily implied that the Emperor was more than aware that actual daemons existed, but was trying to starve them, essentially. All was going swimmingly until some of his sons sided with the aforementioned, very real, Chaos Gods and started a galactic-wide rebellion. The cosmic irony is that after these events the Emperor became the official divinity of the Imperium, and it seems he is now forced to work by his faithful people to save mankind from extinction...
The Tau also qualify — they believe in the power of logic and science, and refuse to believe in the idea of the truly supernatural, even after repeated battles with Chaos, the Eldar, and the Sisters of Battle. These races employ, respectively, daemons and humans mutated by the Dark Gods (and sometimes both in the same creatures), living avatars of a war god present as figures of molten iron carrying a giant sword and an ever-bleeding hand, and what can only be described as divine magic to the point of one of their heroines self-resurrecting and having a few beings tantamount to angels.
There are alternative explanations (they're wrong, but that doesn't mean they don't exist). Mutant humans could have been physically modified like Space Marines, some forms of daemon could be aliens with teleport gear, and Soulstorm shows the Tau hunting for the technology behind the Battle Sister acts of faith (needless to say, without finding it).
This seems to be less that the Tau don't believe in things like Chaos and psykers and more that they're unfamiliar with them. Being inherently less psionic than humans, there are no Tau psykers, so they've never had any experience with things like daemons. They aren't disbelievers, they're outright ignorant. Hence the short story where a Tau army believes they slewSlaanesh — they had no idea about the existence of Chaos Space Marines at the time, so they were unaware that Slaanesh was the name of that band's patron deity as opposed to their commander. It's this ignorance that makes them so dangerous in the eyes of the Imperium; they consider the Tau Too Dumb to Live.
This also makes them dangerous to Chaos as well. As the Tau have a Warp presence that's practically nonexistent, they have an innate resistance if not immunity to daemonic influence. This means that the usual tricks employed against the Eldar or Imperium don't work on them. But if anything, the Tau at best see the servants of the Dark Gods as psychotic maniacs and would rather not tamper with their tools, seeing as they might have something to do with the madness. They even go so far as to kill Kroots who consume Chaos Space Marines.
In Warhammer, the citizens of the Empire (no, not that Empire) largely refuse to acknowledge the existence of the Skaven, a race of maniacal subterranean ratmen. Clearly in a world populated by Dragons, Giants, Lizardmen, the living dead, and goat-headed mutants, five-foot-tall intelligent bipedal rats are just too much. All this after the Skaven have openly attacked the Empire (mostly Middenland) a number of times, and just recently have tried to NUKE Middenheim, Middenland's capital.
According to some sources, the problem is not of their existence, but the idea that they have their own civilization instead of being just another form of mutant beastman.
The Skaven myth is one of the more dubious points of the setting — there are supposed to be more Skaven than humans, they like to abduct cattle and/or humans for slaves and chow, they've fought several wars and they're openly acknowledged by the elves and dwarves allied to the Empire as well as some other human nations directly at the Empire's borders.
The RPG sourcebook about the Skaven tried to make some sense of it and summed its report up with the words "There are two myths about the Skaven: The first is that they don't exist. The second is that anyone believes in the first."
You also got Necoho the Doubter, the chaos god of... atheism... (Worshipmakes him weaker.) Given how long it's been since he was mentioned in canon, he must be one of the powerful gods by now.
The Palladium RPG Beyond The Supernatural featured Nega-Psychics, whose unbelief was so strong it actually (if ironically) disrupts any magic or psionics around them. In Rifts, however, where it's kind of hard to disbelieve a dragon staring you in the face, it became more of a matter of defiance.
Similarly, GURPS has the Mundane advantage, which at its highest level will enforce dull normality around its owner by turning werewolves and aliens into guys in rubber masks and magic into cheap fireworks.
The same thing appears in Unknown Armies. There is an NPC whose skepticism is so strong, he has an antimagic aura. Which, in turn, makes any attempt to prove the existence of the Unnatural to him impossible.
And in Over the Edge with Evan MacDonald, whose skepticism is so great he nullifies anything beyond the mundane around him, be it magic or "just" mad science. In one sample adventure the world is conquered by necromancy, leaving everyone helpless to resist — but MacDonald is still walking around in a bubble of normal reality.
Patches the Hyena from Demons Souls could be considered this. He claims that "praying never killed demons for [him]," when you can directly call down miracles — including "God's Wrath" — at will. He's absolutely right, as the "miracles" are just another form of the Soul Arts. "God" is actually the ancient demon known as the Old One.
Planescape: Torment has the NPC Fall-From-Grace who, in a world brimming with gods and monsters and other such things, is agnostic. She's the party cleric. She's also a chaste succubus and proprietress of a brothel that doesn't involve sex.
Planescape, as mentioned above, is a Clap Your Hands If You Believe setting, where belief shapes reality (and clerical magic is just one form of reality-shaping). Grace draws her power from the Sensate Philosophy.
In Metal Gear Solid 2: Sons of Liberty, Ocelot loudly decries the existence of the supernatural, despite the fact that he used to work with an Ax-Crazy floating psychic, a shaman with flying tattoos, an arguable vampire who could pin people to their shadows, a ridiculously old man who only comes to life in battle and can communicate with forest spirits, a man who could shoot bees, and a ghost; once manipulated an elaborate chain of events involving two (arguably three) non-floating psychics; and is routinely being possessed by a ghost living in Ocelot's transplanted arm. However, this line was added by the translator; in the original Japanese, he only says that technology can replicate the supernatural.
In Metal Gear Solid 4: Guns of the Patriots, however, and as specified in the database, the "possessed by his arm" thing turned out to be real during the events of MGS2, but fake in MGS4. In between he has the arm removed, but he maintains the illusion through hypnosis and NANOMACHINES. Apparently possessing/getting possessed by people is In the Blood. Oh, and Vamp's powers are equal parts nanomachine/badassery.
That being said, The Sorrow, The Pain, and The End did genuinely possess paranormal powers. This is proven simply because nanomachines hadn't been invented in his time.
There happens to be an antitheist in Black & White. None of the godly power you throw at him can persuade him. But that's all right, tossing him about is quite amusing. What's rather interesting is that he was a significant source of belief anyway, if used properly; while he claimed not to believe in you, you could pick him up anywhere he was — even if he was outside of your control, which is something you can't do for anything else in the game, except for your creature. He also extended a small radius of influence around him, so in effect, he was a believer, he just didn't like you.
While not God, in the 3rd Ace Attorney, Edgeworth's disbelief in Spirit Channeling is odd, seeing as how he has sat across from a dead women (who he prosecuted the murder of!) in court...
It's possible this is less honest skepticism and more a kind of willful denial, due to the role that spirit channeling played in the DL-6 trial. It's easier to believe that spirit channeling is fraud than to accept that his father's departed spirit was called back to testify about his own murder and they still couldn't get a conviction...
And to be fair, in the particular case he said that, the murderer turned out to be a human being despite the fact that there was a ghost involved, who tried to kill someone, only to get killed herself. But you cant kill a ghost, so the one who died was the medium that was channeling her.So even Spirit channeling has very physical limitations.
Prince of Persia (2008) featured a protagonist who didn't believe in either of the two gods, despite all the demons he fights and seeing one of said gods try to escape from his prison. When you see inky blackness spilling into the sky and corrupting the planet, and then deny that your antagonist is real, you're just being thickheaded.
In Uncharted 2: Among Thieves, Elena is skeptical of the fact that the artifact that they have spent the entire game after chasing is really supernatural. Despite the fact that in the first game she and Drake fought zombies... created by a mummy sealed in a totem pole made of gold... that is actually El Dorado. Really, Elena, really? Later on Chloe is skeptical as to whether a certain tree they are heading towards is the mystical Tree Of Life, to which Elena responds "We're standing in Shambhala and you're questioning what's possible?"
In World of Warcraft, Gnome characters are limited to classes that practice mundane martial arts (warriors and rogues) or arcane magic (magi and warlocks). The reason? They are a race of primarily atheists who can't play any class that requires faith in a higher power, such as the Light or nature spirits. Despite living with and fighting alongside priests, paladins, druids, and the like.
Their "conversion" actually started in the previous expansion, Wrath of the Lich King. Before the invasion of Northrend, the gnomes were pure science and logic, and though they knew about the Light and other higher powers they preferred to belief in their own ingenuity and were unaware of the history of their race. That is, until the discovery of Mecha-gnomes, the Curse of Flesh created by the Old Gods, and the revelation that they were created by the Titans as clockwork beings who were then made organic by the Curse. "I saw the sign, and it opened up my eyes". The gnomes have begun to open up more towards higher powers, including the Light, and now we have Gnome Priests.
According the the CDeve Q&A most gnome priests are doctors and medics who believe that the healing powers of the Holy Light are just another science they can use to their advantage.
Gannayev from Mask of the Betrayer adamantly refuses to believe that gods exist and has been known to get into massive bitchfights with the priests of Kelemvor over it (one of which you get to jump into. We suggest you don't try to prove Gann wrong, if you value your relationship-related stat boosts). He persists in this delusion even after he meets not one but two gods in person (or switches to Nay-Theism, he doesn't clarify which).
The only thing he doesn't believe in is the wall of the faithless, which, considering the horror it represents, is fairly logical when supposedly good gods are involved in its preservation. It's obvious well before the assault on Kelemvor's domain that he thinks the gods are hypocritical assholes.
The Dwemer fit this as a species of Flat Earth Atheists. They acknowledged the existence of powerful beings such as the Daedra, but either did not accept them as gods or did not consider godhood to be that important. It's not an unreasonable stance to take in truth, since this is a universe where it's possible to ascend to godhood simply by being badass enough to convince the universe you are one.
One Dwemer tale tells of a Dwemer who tricks Azura with a box containing a mirror. After she correctly guesses what the box holds, he opens the box and the mirror makes it appear as if the box was empty,note It's an old magic trick, the mirror is at an angle ergo when you look in the walls of the box are reflected and look like the other sides walls and flaw, so it looks like the box is empty. 'proving' she is fallible and so not a god. He dies that night, a smile on his face. The Dunmer tell a different story: Azura sees through the tricks and strikes him down there and then.
In Oblivion, Ilsi God-Hater appears to be this at first. Turns out she actually worships Mehrunes Dagon, and doesn't want anyone to guess.
"The gods don't do a damn thing. Do they even exist? How could anyone tell? Daedra Lords, sure. They exist. They do things. Bad things, mostly, but things you can see. The gods? They don't do a damn thing. So why do we build big chapels and sit around and mumble, and ask them to save us from this and that? It's stupid. And chapels and priests and folks grovelling on their knees, they're stupid, too."
There's also Ulene Hlervu, castle mage to Count Indarys of Cheydinhal. She scoffs at the practice of worshiping the Nine, stating that worshipping Daedra is more reasonable, though still foolish, because it produces dramatic results.
In Skyrim; the High Elven Thalmor have banned the worship of Talos in conquered nations because they find it absurd that a mortal man can become a god, despite that Martin turned into Akatosh's avatar at the end of Oblivion to stop Mehrunes Dagon. This is actually a cover story for the Thalmor's true desires, they know Talos exists, they also believe that he's a Barrier Maiden holding the mortal plane together, if he stops being worshiped, his power will fade and the world will end, which is exactly what the Thalmor want.
It is heavily implied that people like Ilse God-Hater and Ulene Hlervu are not proper examples of this — they only deny the idea of worshipping the Nine Divines, who created the planet, while acknowledging the existence of the Daedra Lords. Basically every example of the Divines influencing the world are either ambiguous, a matter of legend, very personal incidents that only happens to special people (like Elder Scrolls protagonists), or a combination, while the Daedra Lords influencing the world is a matter of historical record.
The plot for the tenth Touhou game, Mountain of Faith, involves a god attempting to collect the faith of everyone in Gensokyo because she believed the dwindling faith its inhabitants had in its deities would cause massive chaos (that said faith would be an enormous boost to her power was apparently just a bonus). Considering gods in Gensokyo not only have human-like forms but regularly chat with humans and youkai alike (or pelt them with danmaku, whichever seems more fun), either its inhabitants are this trope or don't find it necessary to have faith in beings that are readily defeated by a Cute Witch and a Miko or are Nay-Theist.
Ghostbusters again! By the time of the Video Game, the events of the two films — including two massive ghostly uprisings in New York, a God of Destruction in the form of a marshmallow mascot attacking the city, the Museum of Natural History being engulfed by goo, and the Statue of Liberty taking a stroll through Manhattan — mean that everyone believes the Ghostbusters are the real thing... except Obstructive Bureaucrat Walter Peck, who continues to believe they're nothing but dangerous frauds pulling an impossibly elaborate hoax. It's implied he might be a Gozer cultist that's just faking it to cover his sinister true motivations.Turns out he's not, and after the events of the game, which include another Gozer attack, a supernatural event at the Museum of Natural History at which Peck is personally present and is actually possessed, an island rising out of the Hudson River then sinking back into it again, another massive ghostly uprising — this time including Central Park turning into a massive otherworldly graveyard, and being personally abducted by the ghost of Ivo Shandor who had been possessing the Mayor and personally witnessing the first half of the Ghostbusters' battle with him... he still thinks they're nothing more than dangerous frauds that need to be shut down.
In Star Ocean, after you've visited the king of Van and been told the legend of the Demon World, Iria and Ronixis (your two teammates who are from a scientifically advanced Earth) have a private talk about gods and demons and superstition, and why they shouldn't just accept the supernatural elements of planet Roak and instead look for logical explanations. This flies in the face of the fact that Iria can shoot energy from her hands, while Ronixis has put aside his starship captain commission to become a powerful Heraldric mage who calls down lightning and fire on his foes.
The original Guild Wars campaign (Prophecies) has a wonderful moment where an NPC rants about how she doesn't believe in any Gods after your latest mission goes awry. This is a bit ridiculous, since she's standing next to a person who can revive the dead using the power of faith and lives in a world where praying at a shrine will grant you improved skills. Since the plot of that campaign can be summed up as: "Oh hey, you just made everything worse! Again!" it may be safe to assume that the Gods are helping you just so that they can point and laugh when you fail.
In Guild Wars 2, each race has a view on the gods. While only the humans believe in them, the other races are not atheist per se: the Asura simply consider the gods as part of the Eternal Alchemy, like everything else; the Charr were so scarred by the Shamans that they decide to not revere the gods, but do not deny their existence; the Norn simply have their own deities in the Spirits of the Wild. As for the Sylvari, since they only appeared a few decades ago, i.e. 1300 years after the Gods left Tyria, they just want evidence, making them the closest example of this trope, considering that, y'know, humans will apparently be able to summon Hounds of Balthazar and stuff like that.
The Sylvari have the innate ability to bring huge trees to life, so they aren't completely unreasonable in wanting proof those hounds come from a higher power.
In Quest for Glory IV, Dr. Cranium does not believe in magic, insisting that any claims are merely the result of superstition and that everything can be explained by science. The game even suggests that there's probably magic involved in the healing potions he makes for you, but advises you not to point that out to him.
In Dungeons and Dragons: Order of the Griffon, the heroes are hired by Lord Korrigan of Radlebb Keep to investigate and debunk the rumors of the vampire Koriszegy in the ruins of Koriszegy Keep. He insists that the vampire is a myth and he's only hiring you to debunk the rumors to end the panic. He does tell you that you might meet some minor undead like skeletons and zombies, maybe a ghoul or something. Needless to say, Koriszegy is quite real, and quite dangerous: he nearly succeeds in destroying Karameikos. Somewhat justified by the fact that it's an established fact of the setting that the Thyatian rulers of what used to be Traladara, now Karameikos, tend to hold their Traladaran subjects in contempt as superstitious and ignorant.
The Pretentious Artist from Kingdom of Loathing is one of these. You only find this out if you show up at his place decked out in all of the Bad Moon rewards, and he states that he isn't sure whether he believes in Hey Deze, "even though people go there all the time and bring back souvenirs."
Dr. Aleister Grout, the Malkavian Primogen from Vampire: The Masquerade – Bloodlines firmly believes there's a rational explanation for the fact that he's a vampire and all the obviously supernatural things they can do. It's somewhat implied that this is actually the manifestation of his Malkavian insanity.
Also implied to be his insanity is his methods. The good doctor is a clinical case of antisocial personality disorder taken to eleven.
Arcoscephalean skeptics in the Dominions world are atheistic philosophers who use their acerbic wit to mock belief in the gods. This is quite strange during an epic war between demigods battling to become the one true God. Even worse, the nation of Arcoscephaleitself is ruled by a pretender god who can order the skeptics about.
Another one like Han Solo; Tharan Cedrax, one of the Consular's companions in Star Wars: The Old Republic, travels with a Jedi and was acquainted with Master Syo. Yet, he really dislikes anything that smells of Jedi mysticism and overt Force use in his presence (especially the Jedi Mind Trick). It could be explained by the fact that a Muggle like himself cannot analyze, measure, or experiment with it.
In Wolfenstein, after the mission where BJ receives the Thule Medallion and first learns of the Golden Dawn (a benevolent order of mystics), he can talk to the La Résistance radio operator who claims that the Golden Dawn's leader seeks to "save the world from black magic. Which means he's either insane or an idiot". You could interpret that as BJ keeping the Medallion's powers a secret...if not for the fact that completing the aforementioned mission also causes black clad Nazi sorcerers to fight openly in the city they are in.
Diablo III brings us Leah, whose childhood was spent following her uncle Deckard Cain, who was trying to research ways to prevent the forces of Hell from bringing about the End Times. In fairness, Deckard admits that things were peaceful the last twenty years, but one would think that she might give her uncle the benefit of the doubt after seeing zombies rise in front of her and experiencing her own supernatural powers. She only decides Deckard might have a point after he is murdered by cultists and then finding out that one of her companions is a literal Angel.
In Ghost Trick, the justice minister loudly denies the existence of ghosts, even after Sissel goes back and saves him from dying of a heart attack. Then it turns out he was mostly trying to convince himself, after being manipulated by Yomiel into signing Jowd's execution order and spending the last few weeks covering it up.
In Ozy and Millie, an ambassador sent to Greater Llewellynland to discuss foreign policy with Llewellyn, a dragon. Said ambassador refused to believe in dragons. Hence, he mostly hung around the castle and annoyed Ozy.
This is actually based on Jetfire's personality in the comics. It's a long-running implicit joke that he believes in some odd kind of evolution which is obviously ridiculous (although the levers-and-pulleys thing was actually canon at one point). The above comic is not exaggerating.
The fact that he was made by a very intelligent designer (Shockwave) in the Marvel comics makes this even funnier.
It should be noted however that in the continuity where Jetfire's atheism is most often brought up (the Dreamwave comics), his atheistic beliefs are slightly more justified since there was no clear modern day evidence that said creator ever existed (let alone that he was the planet itself). He still counts though, since he refuses to believe in any sort of mysticism despite the fact that weird supernatural shit happens to him on a recurring basis.
Likewise, Dreadmoon of the Insecticomics is an atheist and skeptic. Somehow he manages to reconcile this with the fact that his commander has an immortal spark, people can and have been brought back from the dead, and they have done battle against the powerful minions of a chaos god who is the closest thing Transformers have to the Devil.
And now they're doing battle against the chaos god himself. This does not seem to have caused any crises of faith.
Leslie insists that there was no historical Jesus even after Galasso, who had been proven to have the ability, brings him back from the dead, despite the fact that his teachings, appearance, and demeanor all line up with euhemerist study of the Bible rather than modern Christian caricatures, getting so frustrated with her cognitive dissonance that she physically attacks him.
In 8-Bit Theater there's a Running Gag with Thief believing dragons are extinct despite encountering (and getting mauled by) them several times. Eventually Red Mage asks why he keeps saying this. His response?
In Gunnerkrigg Court, Coyote berates humans for being so preoccupied with trying to find a cause or meaning behind everything that they place their own imaginary answers behind anything they can't explain; Coyote is essentially criticizing a form of the "god of the gaps" argument. What makes this strange is that Coyote's whole point is that he doesn't exist, which doesn't really add up seeing as he himself, who has been shown to exist in-universe, is explaining this argument to Antimony.
Coyote himself states that he, and all other supernatural entities, are merely physical manifestations of Man's belief, making Man the most powerful creature in the world above all others.
Eridan lives in a world which canonically contains ghosts, telekinesis, clairvoyance, psychic mind control, dragons, telepathy, time-travelling demons, trolls who spontaneously sprout butterfly wings enabling them to fly, Cosmic Horrors, vampires, and sgrub/sburb itself. But he doesn't believe in magic. That stuff's fake.
Cronus also follows the same path, though it's justified, as he USED to believe in magic, but someone decided to take a sledgehammer to his faith.
In Slightly Damned, Rhea (and many other Medians) apparently are skeptical about the existence of divine beings, despite the fact that angels, demons, and gods are just walking around in the open. Somewhat justified, however, as it's implied that these things are unique to Riverside, and the 'verse's equivalents of God and Satan really have never been seen.
The Dreaming Witch from City of Reality, despite living in a world of magic, is convinced the magic she does is impossiblenote ironically, she does seem to be breaking the rules of her world, but not in the way she thinks, and hence she must be dreaming. Needless to say, she's a wee bit mad.
1/0 featured the character Marcus, who became so angry at the comic's creator Tailsteak that he willingly acquired a fourth wall — an inability to hear Tailsteak, see the comic's layout, have real-world knowledge, to realise in any way he was a character in a comic. Marcus remained stolidly convinced he was the Only Sane Man despite Tailsteak's continuous creation of life, inventing laws of physics, and generally interfering with the comic's world in an obvious fashion. Ironically, to rationalise all the ghosts and golems and such, Marcus eventually had to create his own increasingly-convoluted religion. Eventually, he reaches such levels of Strawman Political (very clearly representing atheism, agnosticism, pantheism, and polytheism at various points) that Petitus chews out the Christian author for his anviliciousAuthor Tract.
Roger, the main character of Go Fish, is a great example of this trope. Despite being recruited to be a god's contact on Earth, meeting various gods and angels, and actually visiting the realm where the gods live, he still identifies himself as an atheist in a recent comic.
The mechans are proponents of the scientific method in a world where trying to quantify or manipulate the properties of magic can result in new species of undead, horrible magic artifacts, or the ruination of entire countrysides.
There is also a god, Arkhanos, who encourages their followers to not be 100% sure of said deity's (or any other deity's) godhood. Or gender, for that matter. Arkhanites like to point out that while divine magic works and gods have made well-documented appearances, it's possible that they're simply much better at magic than "mortals".
The best example of this is Steff, who is a follower of both Mechanism and and Arkhanism despite being in a relationship with both a half-demon and a semi-divine harvest spirit who regularly converses with her creator deity.
The MUniverse contains multiple religions, each with its own distinct (and in some cases conflicting) mythology/theology, all of which are apparently real. So it's fairly easy to see how people might get confused. To quote the author:
In most fantasy worlds, because "the gods are real", there's one set of myths which are only myths in that they're mythic in scope... they're essentially true and everybody knows them and agrees on them, and if there's any dissent it's a big story point because either the dissenters are eeeeeevillll or they're secretly the good guys. Even if the elves have one set of myths and the dwarves have another, it's only because they have different gods and their myths only deal with their corner of the world. With everything else they fight about, you rarely see the dwarves and elves falling out because one believes the world was made from the bones of Fireaxe Grimbeer and the other thinks it was fashioned in seven days by Emostar Vaguelygay, because those gods are real in the story and therefore not subject to this kind of disagreement. I don't really buy the logic there. Our world is made of real and we can't often agree on any two things inside it. Ignoring the possibility of any actual divine/supernatural stuff existing in our world, all of our conflicting myths and legends came about because of real, (at one time) verifiable events: wars, people, seasons, animals, whatever. Adding another class or two of things to those lists wouldn't change the essential nature of the beast, which is that 1) we like to make stuff up when we don't know something and 2) we frequently don't know shit.
In Metamor Keep Metamor's High Priestess, Raven hin'Elric believes the "gods" she regularly converses with and draws power from are really just entities with a lot of magic that they are willing to lend to others .
By the time of Metamor City, written by Raven's creator, she seems to have been proven right as her former student Mirai has pulled the gods of light and dark down to earth and taken most of their power. And then started a new religion that worships the same monotheistic god as the setting's version of Christianity.
In the episode, "The Fortuneteller", Sokka refuses to believe that psychics are possible, despite living in a world where people widely practice magical manipulation of elements (including his traveling companions) and knowing that the spirit world is very real. That said, fortune-telling is not otherwise seen within the cosmology of the universe, so this may be like using the strong and weak nuclear forces (as well as other real world weirdness) to justify a belief in magic.
Another good example is Season 2, Episode 4 "The Swamp." Despite knowing that spiritual locations do exist and witnessing first hand the mystical powers of the titular swamp (including a giant tornado appearing out of nowhere and smacking them out of the sky when they refused to land) Sokka refuses to believe that the place is anything other than a perfectly mundane swamp.
When confronted with how much of what Aang does defies explanation he Hand Waves that avatar stuff doesn't count.
Hawkgirl, who does not believe in anything supernatural despite winning a fantastical battle against Doctor Fate and personally knowing a zombie, not in gods despite meeting and killingIcthultu, and not in souls despite being taken over by the literal soul/s of ancient Snake People who put their souls into a gem, and knowingWonder Woman.
Wonder Woman and Aquaman are used by the Writers on Board to dump the idea that faith is a hollow thing that brings happiness when in actuality Wonder Woman is based in the blessings of Classical Mythology with a real Hera and bracelets made of Zeus's Aegis on her wrists, while Aquaman stated that his Atlantis was based in the use and misuse of magic, resulting in his trident and in a temporary age of peace for the Earth from monsters like Icthultu.
The Flash points out the absurdity of such skepticism in one episode when Green Lantern doubts his word that a gorilla talked: Hey, we've both got a Martian's number on our speed dial. I think I deserve the benefit of the doubt.
Although God and Jesus Christ have been shown to exist, and Homer has had numerous run-ins with the Almighty, he's still able in the episode "HOM-R" to construct a mathematical proof of God's nonexistence while trying to devise a flat tax proposal. This is just another of the many times where the show openly ignores continuity for the sake of a quick joke. Since he has an IQ of 105, it's likely the proof is not valid, but it's upsetting enough that Ned Flanders can take one look and think it is.
He was just probably trying to mess with Flanders though. Intelligent or otherwise, Homer is still Homer.
Ironically Ned Flanders as well. Set 30 years in the future Ned remarried Maude's ghost. She explains to him there is no heaven, just an empty void. All Ned does is chuckle and ask the Simpsons, "ain't she pretty?" One version of Hell is a void and the absence of God. Could be there is a God but Maude had gone straight to Hell.
In the Adventure Time episode 'Wizards Only, Fools', it is revealed that Princess Bubblegum doesn't believe in magic. Despite having used magic talismans in the past. And regularly being targeted for kidnapping by a wizard.
More accurately, she accepts that the things typically considered "magic" such as wizardry do exist, but is of the belief that all "magic" is just natural phenomenon with scientific explanations that nobody has been able to figure out yet.
In the episode "Cartmanland", Kyle loses faith in God. This is despite the fact that the boys have met Jesus and Satan in the past. In one episode, they even meet God itself. Although, it could be that he just believes that God doesn't care, as opposed to God doesn't exist. Never mind that he is Jewish, while knowing that Jesus exists and has holy powers. Also, it isSouth Park. There are actually a minority of Jews who believe in Jesus in Real Life, although other Jews might be skeptical if they can still be called "Jews" after that. In general, they believe that Jesus was a Messianic Archetype, but otherwise practice Judaism, which probably makes them quite close in practice to some of the earliest Christians.
They really, really aren't Jews. Not only is it quite clear that most of the actual recruiters for the Messianic organizations actually members of the mainline Christian parent organizations, but there aren't even enough actual Jews to point out that the way they "practice Judaism" is more of a Christian's idea of how Judaism is practiced. For one notable example, Jews for Jesus actually advertizes that it believes in original sin as a commonality with mainstream Judaism. Original sin is an exclusively Christian interpretation.
Additionally, Mohammed, Buddha and Joseph Smith also exist and have superpowers in "Super Best Friends". They Fight Crime! Despite this, in "All About Mormons", Stan found the entire story of Joseph Smith and Mormonism impossible to swallow.
The real God is, for lack of a better description, a bunyip. And he's also a Buddhist. Who only lets Mormons into Heaven. South Park is odd like that...
In "Hell on Earth 2006" Satan hosts a huge Halloween party on Earth (marking at least his third public appearance on the surface). The episodes immediately following? A 2-part story arc all about how Richard Dawkins and Mrs. Garrison turned the entire planet into straw atheists.
Also applicable is "Red Hot Catholic Love", where most of the boys' parents became atheists and celebrate over the fact that the Vatican was destroyed, despite the fact that it was destroyed through supernatural means and a giant Queen Spider is clearly present- plus, you know, again the fact that they all knew God, Satan and Jesus were all real and had seen them in person.
This actually may be a bit of Author Appeal. Matt Stone has in interviews given conflicting answers on whether he believes in God, and Trey Parker says he does believe, but he doesn't understand it. This could be a way of expressing how they themselves don't really know how God in Real Life would work.
Mandy is rendered immune to the Tooth Fairy's powers by revealing, to his face, that she doesn't believe in him.
Brian of Family Guy is a professed atheist despite the fact that God and Jesus are frequently seen in Quahog and the former once smited the family with Exodus-like plagues. However, it isFamily Guy. And he is an Author Avatar.
What's interesting is in the episode "If I'm Dyin', I'm Lyin'" Brian is the one who points out the plagues to Peter and then slaps him declaring that the reason things are happening is "God...is...pissed!"
In the episode "I Dream of Jesus", Jesus had dinner at the Griffin household, among other interactions.
This reached its height of ridiculousness in "Family Goy" when Jesus showed up at the Griffin house again just to tell them that all religions are crap. Brian then gloated that he'd been proven right... because Jesus said so.
Lampshaded in "Jesus, Mary and Joseph!": when Brian calls the Nativity story fictional, Stewie remarks: "Jesus lived with us, like, for a week! What more do you want?"
Doc Saturday from The Secret Saturdays actively disbelieves in magic despite being married to someone who uses magic (and wields a magical fire sword), having a son with supernatural powers, and continually doing battle against things like evil alternate reality doppelgangers, killer salt monsters, and an evil Large Ham out to conquer the world by unleashing a mythical god of evil.
In an episode of SpongeBob SquarePants, Squidward says he doesn't believe in ghosts (or more specifically the Flying Dutchman), which is odd considering the Flying Dutchman appeared to the entire town in the Halloween Episode and Squidward was zapped over and over and tortured by the Flying Dutchman in another episode. To be fair though, Spongebob has almost no continuity worth mentioning.
In the Batman Beyond episode "Revenant", an invisible force is terrorizing the school, which Terry's friends think is a ghost. This conversation ensues: By the way, he's right. It's Terry's old classmate using his psychic powers, not a ghost.
Bruce: These people believe anything they can't explain is magic.
Terry: Naturally, you don't believe in that kind of thing.
Twilight Sparkle of My Little Pony: Friendship Is Magic comes off this way on occasion, refusing to believe in anything supernatural despite living in a land of magic. Her friends are quick to point out that she can do magic, so what's the difference, and she usually has an answer for why magic is real and something like a curse is not.
Twilight is a believer in Magic A Is Magic A, even though this is manifestly not how magic actually works in Equestria.
To put that in perspective: she's gone against shapeshifters who feed on love, a demon of the night, a literal god of chaos, and is best friends with Pinkie Pie, who breaks just about every rule in the books for giggles, but time travel? No, sir, that is the line!
Though she never actually disputes the idea of time travel, just the idea of two Twilight Sparkles, losing one sanity point and declaring that Other Twilight is not scientifically possible. In fact, the time travel thing was mentioned after that, to which she begins to ramble about Future Twilight possibly having been involved in an "Epic Pony War".
Considering it proceeds to create a stable time loop... Maybe ignorance of Time Travel is a good thing. She'd waste it on the first thing that ever came up, like going back in time to tell herself not to worry about the stuff she was told by Future Twi... Oh, wait.
Kid Flash in Young Justice. He's perfectly okay with pocket dimensions and Mind Control existing, he just thinks everything has to have a scientific explanation behind it. Partly justified in that one of the Flash's enemies was a Time Traveller posing as an Evil Sorceror (and actually served as The Dragon in the episode in question) and because this skepticism seemed to only last a single episode - on every other occasion magic shows up, Kid Flash is (to all appearances, at least) a lot more accepting of the reality of it all. Also, by the end of that first episode where he denies the existence of magic, it's pretty clear that Wally knows better and just doesn't want to admit being wrong.
Daria claims not to believe in God and the supernatural in the fourth season episode "Groped by an Angel". This despite the fact that in the previous season she met the Anthropomorphic Personifications of various holidays (though they did at least have the excuse of coming from a Pocket Dimension a la The Mighty Thor). There's also the fact that according to the Beavis and Butt-Head episode "It's a Miserable Life" God and guardian angels really do exist, but Daria herself wouldn't have any way of knowing this. That's assuming that the holiday episode was even canon. Every other episode (well, aside from the musical one) takes place in a normal world, so the holiday one is very out of place and it's presumably non-canon, similar to the Treehouse of Horror episodes of The Simpsons.
Isabella: But Buford, you've been in a space ship. Several, actually.
Buford: I'm a skeptic.
Fridge Brilliance: They were talking specifically about aliens, and presumably Buford was never around in an episode that focused on aliens.
Pick any Christmas movie or Christmas Special in which Santa Claus is real and actively delivers presents to a large fraction of the world's children, yet the vast majority of adults do not believe in him. Review the situation: Mysterious packages show up under Christmas trees that Mom and Dad certainly don't remember buying. Little Sally in the hovel next door ends up with an expensive doll in her stocking despite her parents barely being able to afford necessities and keeping the doors locked for fear of burglars. Yet despite these otherwise inexplicable occurrences, people dismiss Santa as a fairy tale or "stuff for babies."
Worse, in the Christmas movies/specials where Santa Claus not only exists, but doesn't even actually hide his existence — to the point where you'd easily be able to see the man just by waiting outside on Christmas Eve, or even by telephoning the North Pole.
Taken to hilarious extremes, for the sake of a joke, in one Rankin-Bass movie in which a young atheist mouse says he doesn't believe in Santa...despite Santa having a phone number and a staff of people to answer any calls. When he says this, the athe-mouse's dad gives him a look that is the 70's animated special equivalent of "Wow you're a spectacular retard". This is a world where Santa is so clearly and explicitly real that when he tells the town's mayor he won't come here this year due to the athe-mouse insulting him in a newspaper (yes...) the mayor attempts to build a huge beacon to tell Santa how much they're really, really sorry. In other words, Santa is at least as real as any other businessman the town is trying to curry favor with. And the athe-mouse kid still didn't believe it till his father showed him everyone else in town did. The irony? Athe-mouse is the SMART one in his family (by his reckoning). Yikes.
But when trying to convince the-mouse, his dad uses arguments similar to theists, trying to make his son have faith in things in which there is no empirical proof (the song "Give Your Heart a Try,") despite the fact that there is empirical proof of Santa in this universe. It's even stupider in The Year Without a Santa Claus when a bunch of children announce that the newspapers have reported that Santa Claus is a taking a day off and ten seconds later say that they don't believe in Santa. Santa himself sings a song to convince one of the children of his existence: "I believe in Santa Claus / Like I believe in love..." not "I believe in Santa Claus / Because I saw his picture in The New York Times..."
The same would apply to the Easter Bunny and the Tooth Fairy, where they also actively deliver presents to children.
An old Soviet joke runs something like this: A communist (and thus staunch atheist) died. However, he had been a good man in life, and God was willing to forget his unbelief, provided that he spent an equal period of time in Hell and Heaven. He served his first year in Hell, and Satan said to God: "Take this man quickly - he has turned all my demons into Young Pioneers! I must restore order!" After spending a year in Heaven, God took him back to Hell, where he had this conversation with Satan:
Satan: Lord God, it is my turn now.
God: First of all, don't call me Lord God but rather "Comrade God". Second, there is no God, and third, hurry up or I'll be late for the Party meeting.
In the Spanish version of the joke, it's Karl Marx himself who dies and is sent straight to Hell, where he promptly starts getting rank-and-file demons to make common cause with the damned. Satan tries to get rid of him by shipping him into Heaven, half-expecting the guys Above to reject him. When he goes up to Heaven to check after a few days, it's Peter who greets him and informs him that "there is no God".
In this Spanish comic strip◊, an atheist climbs into a tree to escape a bear. An angel flies down to meet him, and the man insists he's not going to convert just because an angel saved him. The angel then reveals he came to help the bear, who is a Christian and is thanking God for this meal.
There are quite a few medieval jokes about the highly textual and logical nature of rabbinical debate that always end in God coming down to tell the "winning" rabbi that he's wrong, only for the rabbi to argue right back and force God himself to admit that he has the more logical interpretation.
Placebo-based research was first developed to test the methods of Franz Anton Mesmer, which were based on "Animal Magnetism." This was despite almost all patients reporting feeling a sort of aura and going into convulsions when treated. It wasn't until the medical establishment blindfolded a boy and brought him to tree after tree (many of Mesmer's followers operated by magnetizing trees) that they figured out that merely telling someone that a tree was magic was enough to get him to perceive magic.