Atheists in real life can be a rather diverse group. After all, the only thing confirmed by the label "atheist" is that the person does not believe in any gods. It's like trying to make a coherent generalization about people who don't like baseball.
In fiction, however, while it is reasonably common to see a character who is never shown practicing or even mentioning religion, it's generally only characters with a fair degree of cynicism and bitterness who can state outright that they don't believe there are any gods. Some of the more common character traits are:
Atheists only seem to have arguments against their culture's predominant religion, most often Christianity, and to a lesser extent, its brethren Judaism and Islam. They'll have nothing bad to say against Eastern religions.
Atheists are smugly convinced of their own intellectual superiority and usually blinded to the "truth" by their own elitist pretensions. Usually, they are shown as being Not So Different from their religious opponents, especially the more fanatical ones.
Edward Elric, a bitter young man who lost his faith in any kind of benevolent god when an attempt to resurrect his dead mother goes horribly awry and becomes very grouchy and condescending when it comes to religion. While Ed actually does seem to believe in God (seeing how he basically got his arm and leg stolen by him), he just doesn't like him. In the first chapter of the manga, Ed mutters that he's agnostic when Rose goes on about the local priest's miracles. There's also a later chapter on the Ishvalan war, in which the religious leader of the country turns himself in to save his people. King Bradley declares that his life is not worth an entire nation and laughs that if their god exists, why doesn't He strike him down for the genocide. Shortly after, Mustang and Hughes discuss Ishval's religion and how their god seems to have abandoned them.
King Bradley goes even further, repeatedly stating that there is no God but the ones that humans make. This adds yet another dimension to his final battle against Scar, a devout man whose life was destroyed on Bradley's orders.
In the 2003 anime version, Colonel Roy Mustang vacillates in the direction of atheism, and has a notably traumatic past. He's a little world-weary and something of a Jerk with a Heart of Gold. He remains a heroic character through to the end, at one point defiantly shouting "There is no God!" at his would-be savior of a nemesis. Said nemesis gets a rare villainous Shut Up, Hannibal!, though, by saying, "Maybe not, but there's a Devil, and you alchemists are it." Ironic for the Flame Alchemist to get burned.
Simon from Tengen Toppa Gurren Lagann plays this one to some degree during his Heroic BSOD: while still mourning Kamina's death, at one point he tells former First Church of Mecha member Rossiu something along the lines of, "Could your God prevent Bro's death? Oh, yeah, I forgot, it's just a Ganmen!" He eventually apologizes for being rude.
Setsuna F. Seiei, the main characte, is a former Muslim who lost his faith when fighting as a Child Soldier terrorist insurgent and witnessing the horrors of war. This faith has been replaced with a faith in the concept of "Gundam" that is anything used for "the erradication of war" be it mobile suits or those piloting them hence Setsuna declare's himself not only a Gundam meister (pilot) but "Gundam". It helps that the first Gundam he saw after losing his faith had a definite angelic vibe to it.
It also helps that he was manipulated into becoming an insurgent (and killing his own family) by someone appealing to his Muslim faith to justify it. And that said manipulator is one of the most thoroughly evil and self-serving characters the Gundam metaverse has ever spawned, who did the whole thing because he was getting paid and loves chaos.
Subverted by Roronoa Zoro in One Piece who was revealed to be an atheist during the Skipeia arc, but not due to his tragic past, and has no problem at all with faith in general. Furthermore, he also stated that if god did exist, he would like to meet him because he or she would be a Worthy Opponent. He's just that badass.
Foh from Bt X is a subversion of this. Having given up on the ideals that gods exist due to witnessing war from a very early childhood, he eventually came to realize that does not mean he can be a jerk. The fact he's responsible for getting one character's sister killed, an issue he's willing to let himself get killed over in spite of the fate of the world hanging in the balance possibly is a driving factor. He strongly believes in mercy and compassion, vehemently hates fighting because it brings only tragedy to people, and runs an orphanage and raises kids right. He even wears a religious memento from his friend's dead sister. It helps that Masami Kurumada, the series's author, is himself an atheist.
Pretty much everyone in Black Lagoon are all stated to be atheistic, of the 'lost their faith during their childhoods' type. In Revy's case it was replaced with a nihilistic materialism (in her own words: "Money and guns. As long as you have those, the world's a great place."), while Hansel and Gretel went utterly insane by the injustices done to them and became convinced the only purpose behind existence is to kill or be killed. A somewhat more reasonable atheist appears later, as a former Communist aiding a fundamentalist Muslim organization, despite not believing in a god, because he misses having a cause to fight for.
Baran the Emperor of Light, a villain from the final chapters of the Fist of the North Star manga, whose disbelief in God comes from the fact that his dead sister died from a curable disease because she refused to take the medicine he stole for her. His non-belief later drove him to start his own evil cult.
Black Butler gives us Ciel Phantomhive. He used to be such a sweet, happy boy, before his tenth birthday, in which people came into his home, murdered his parents and most of the staff, including attempting to kill the house steward in front of him, set his home on fire, presumably to dispose of any evidence Scotland Yard might find; kidnapped him, where he was kept literally in a cage with other children his age, implied to have been gang-raped on a near-nightly basis, and then ultimately denounced his faith during a ceremony in which he was to be the sacrifice. This is how he came to get Sebastian, who is one hell of a butler. Ciel, three years later, still has an avid disbelief in God, and in fact, if he is not a Hollywood Atheist, might just be a borderline Satanist thanks to his complete trust in Sebastian.
Gundam Wing gives us a rather odd example, in the form of Duo Maxwell. Duo wears a clerical collar and Creepy Cool Crosses, but he states in Episode Zero that he believes in the Grim Reaper but not God because "I've never seen a miracle, but I've sure seen lots of dead people!" (Amusingly, the Cool Old Guy priest concedes that it's hard to debate his logic.) In Frozen Teardrop (set 30 years down the line) he appears to become a preacher, but It's more of a front for his Bounty Hunter work than anything else.
Given that Batman has seen demons, been teammates with angels, and in general encountered the mystic enough to know that some kind of supreme being exists, Batman's position is sometimes written not as "There is no God" but "When I finally meet God, He'd better have a really good explanation for all this crap."
At least in the Bronze Age, he is definitely not a religious practitioner. When asked by Dr. Leslie Thompkins if he ever prayed, he replied "No. Not since that night."
According to Batman Beyond, Batman only believes in Gods he has evidence for. For example, he is obviously not stupid enough to deny all the angels, gods, demons, zombies et al. he's seen are not real; however he's quick to point out that he doesn't believe in most claims of them, because he's experienced enough to know the real Gods and angels and demons and suchlike from the fakes. Batman certainly doesn't worship God or practice religion, at least from what is seen in the show.
Freddy Krueger-esque Mister Rictus from the comic book miniseries Wanted. He was the most pious of Christians until he died on the operating table after an accident. After seeing what lay beyond, i.e. nothing, he went completely crazy and started doing whatever the hell he felt like with no restrictions or morality whatsoever. Of course the fact that the accident scarred him to a ridiculous degree may have contributed. He is basically the personification of one of the most common atheist reaction to the "Atheists have no moral code" claim; namely "If faith is really the only thing that keeps someone moral, then that someone has problems."
Warren Ellis has used a similar approach a couple of times. In Stormwatch, there's a character called The Eidolon, who's died and returned to let everyone know that there's nothing beyond this life. Then there's an early issue of Planetary with a Hong Kong ghost cop (possibly cop ghost) who's come back with a similar message. ("There's just us." "Did he say justice?" "No. 'Just us.'")
The Kree from the Marvel Universe claim to have mathematically disproved the existence of God and teach it to kids just after toilet training. The fact that All Myths Are True in the Marvel Universe means they're crossed with Flat Earth Atheist
Justice Society of America: Michael Holt, aka Mister Terrific: He's a compassionate and heroic man who just happens to be an atheist, and good friends with Doctor Mid-Nite, a devout Catholic. Complicated by the presence of several divine beings in the The DCU, several of whom he has worked with, but there are various justifications given for that. Developments with Mr. Terrific (especially meeting his Earth-2 mk II counterpart) have pretty much established that he was indifferently religious until his wife died, at which point he got pissed off at God; had she survived, he would have found a profound faith from that miracle, so he's playing this trope straight now.
Madcap in Ghost Rider comics doesn't believe in Zadkiel (the evil angel who took control of heaven) even though he is directly working for him. And note that this takes place in the Marvel universe, where, decades ago, the Gorgon mathematically proved the existence of God. That said, Madcap is one of the most tragic examples of this trope, a devoutly religious young man who saw his entire congregation die horribly in the accident that gave him superhuman powers. Needless to say, such incidents didn't exactly help his mental stability. However, it's also worth noting that the atheist facet of his personality was only introduced in the Ghost Rider comics.
In one Punisher / Wolverine crossover there was a villain called "The Atheist", whose stated complete lack of belief in anything gives him free reign to do as he pleases.
In Marvel Comics, the Uncreated are an alien race who know themselves to have been created by a "god" (this being the Marvel Universe, it's unclear whether this was a Physical God or a Sufficiently Advanced Alien). This gave them an overwhelming inferiority complex, and so they murdered this being. They then became Scary Dogmatic Aliens and launched a genocidal reverse-crusade to exterminate all civilizations who worship any sort of deity. The Starjammers defeated their fleet by tricking them into believing their god had returned. They committed suicide.
Chick Tracts feature Hollywood atheists, specifically Hollywood from the 1950's. On a good day. No wimpy excuses in the Chick-y-verse, and any atheists who isn't hearing about this Jesus fellow for the first time in their lives and converted on the spot is a Card-Carrying Villain. Oh, and this is all supposed to be a realistic portrayal of the world. At least atheists can rest assured that just about every other belief system except the author's gets the same treatment.
Subverted in the one-shot comic A Momentary Lapse of Unreason. A main character begins to question God because his parents died in a car crash, but through questioning he begins to base his atheism on logic and theological arguments rather than misery.
In End of Days, the protagonist has completely given up on God after his family was killed by mobsters. Admittedly, he gets a bit better reason to convert than 'one good thing happening', seeing how Satan stops by his apartment for a chat.
The protagonist of Contact, making a decent example of the dead sibling variety. With several Fundie Strawmen on the other side (one of which is a terrorist bomber, the other a sleazy politician named "Richard Rank"), this movie goes for the Golden Mean Fallacy.
McCord: Well, you know when you want something really really bad and you close your eyes and you wish for it? God's the guy who ignores you.
The hero of Dracula Has Risen From The Grave just happens to be an atheist, with no tragic past. He eventually converts by the end because he sees Dracula getting repelled by a cross and it gives him reason to believe in God
Nicky from Parting Glances who is living with AIDS, although to the film's credit we're never actually told that his illness and his lack of religion are connected.
"God, I hope you don't exist, but if you do, you've got me pissed!"
Mel Gibson's character from Signs is the very embodiment of the first type. It's unusually sensible in his case since his faith seems to come from his belief in predestination. He's unable to reconcile his wife's particularly horrible death with his belief everything happens for a reason. Although when he later prays to God, he says "I hate you" implying he's more of a misotheist.
Starship Troopers 3: Marauder has a lot of fun with this theme. The fascistic Federation regards religion as potentially subversive. The heroine, Captain Lola Beck, reflects this view and cracks down hard on fellow soldier Holly Little's Christian prattle. She even questions the sanity of her superior, Sky Marshall Anoke, when he also claims to believe in God. Beck changes her mind when, after facing imminent death from a giant alien Vagina Dentata (the "God" Anoke was really referring to), a host of "fiery angels" (a team of space-dropped, Powered Armor-wearing ass-kicking Marauders) come to their aid in response to their prayers. Likewise the Federation is impressed at how Sky Marshall Anoke obeyed the alien god's orders without question, and decide there must be something to this religion stuff after all. So the Federation officially declares that God does exist. And naturally, He's a citizen of the Federation!
Slade Craven, the main character of Turbulence 3: Heavy Metal and a Marilyn Manson expy, is never stated to be a satanist, but has implied atheism. At the end of the film, having gone an incredible distance on nothing but his own competence, he has to convert to Christianity, in a "No Atheists in Foxholes" moment before he can resolve the plot.
John Koestler, the protagonist of Knowing, has lost his faith after his wife died in a hotel fire. He's made a believer again by the apocalypse, even though he saw the angel-boat leave without him.
The medic, an atheist, is portrayed as bitter, selfish, and eager to kill Nazis under any circumstances. In contrast, the sniper, a Christian of an unspecified sect (but probably a Mormon) is compassionate, even to Acceptable Targets like soldiers of the Third Reich. Naturally, the bitter atheist is converted in the span of an hour and a half, and the saintly Christian gives his life for his comrades.
In Fight Club, although Tyler Durden's religious beliefs are not deeply explored, he at one point remarks that Our fathers were our models for God. If our fathers bailed on us, what does that tell you about God? It's possible this was from the book, but he also posits that if there is a God, it's better to be hated by him than ignored. Note that, here, "God" is a metaphor for absentee fathers. Durden's actual theological opinion is wide open.
Fairly stereotypical example with Jack Nicholson's character in The Bucket List. He's bitter, cynical, extremely unpleasant to most people he interacts with, and claims to envy people with faith even if he doesn't understand what it's about.
In Bergman's Fanny and Alexander, the title kids endure a lot: their father dies, and their mother marries the rigid Bishop Vergerus. Leaving behind the comfortable lives they'd known with their affluent family, they move to the Bishop's austere home (like a dungeon, with bars on the windows), and give up all their possessions. Alexander's defiance frightens Vergerus, who thrashes him brutally (perhaps the boy's imaginative explanation for the death of the Bishop's first wife wasn't such an outrageous fiction?). After a miraculous escape—but the children's safety isn't certain, not permanently—Alexander muses, "If there is a god, then he's a shit, and I'd like to kick him in the butt."
Whilst it's not made particularly explicit in Quills that the Marquis de Sade is an atheist rather than a straight-up God-defying heathen as believed by most of the characters, he does make several slightly Hollywood Atheist remarks. These include him mentioning to the Abbe that he "has been to Hell", during his fighting in the Napoleonic Wars, whereas the Abbe has "only read about it." Also: "Why should I love God? He strung up his son like a side of veal. I shudder to think what he'd do to me."
Admiral Motti from A New Hope is pretty much the Recycled IN SPACE! equivalent of this, as far as expressed contempt for the Star Wars universe's equivalent of religious belief goes (Motti even calls it a religion). Vader chokes him for his insolence.
Han Solo is a good example, as he ridicules the Force at first and later comes to believe in it or at least respect it.
Han: Kid, I've flown from one side of this galaxy to the other. I've seen a lot of strange stuff, but I've never seen anything to make me believe there's one all-powerful Force controlling everything. There's no mystical energy field that controls my destiny. It's all a lot of simple tricks and nonsense.
In the movie The Rite, the main character is a priest who doesn't actually believe in God (he joined the seminary to get a free college degree). Even after he sees a girl possessed by demons who speaks in tongues, contorts her body into impossible positions, and her voice changes completely, along with her vomiting up the nails used to crucify Jesus, he still claims it was just a hoax to cover up her being molested.
Bethany, in the film Dogma is pretty much the first kind due to being infertile and the resulting divorce. By the end, she gets a bit more concrete evidence than most Hollywood atheists.
Ichabod Crane in Sleepy Hollow is an example of the first kind, as his father killed Crane's mother by shutting her into an iron maiden for seemingly practicing some manner of paganism.
The Christian film The Atheist is about an atheist man taken on a trip by Jesus to examine the issue of faith. Apparently all atheists are rampant sinners who do just about everything a Christian would think of as wrong.
Riddick: "Think someone could spend half their life in a slam with a horse bit in their mouth and not believe? Think he could start out in some liquor store trash bin with an umbilical cord wrapped around his neck and not believe? Got it all wrong, holy man. I absolutely believe in God... and I absolutely hate the fucker."
Averted in The Ides Of March, George Clooney's character is openly non-religious and states he cannot know if God or an afterlife exist, but also acts non-bitter, is entirely respectful of others' belief and states in the film that even if he doesn't share your religion, he'd fight to the death for your right to hold it.
The filmmakers of The Ledge deliberately wanted to avert this trope for the protagonist, who is an openly atheist man that didn't come to his lack of belief due to trauma, leads a fairly happy life and doesn't convert in the end. Unfortunately, the hero becomes unsympathetic for other reasons.
In The Matrix Reloaded, Captain Morpheus is being dressed down for convincing one of the ship captains to remain and wait for word from the Oracle. When Commander Locke tells him that he (Locke) doesn't believe in Morpheus's faith, Morpheus states that his belief "doesn't require that you do."
Gestapo Investigator Robert Mohr from the German film Sophie Scholl is a spineless legalist who toes the party line, in contrast to his prisoner Sophie, an idealistic, devout Lutheran who believes in the equality and value of every human life, and who claims that the German people really want peace, compassion, and God, a position Mohr finds incomprehensible.
Ray Stanz of Ghostbusters is one of the few "honest" atheists portrayed in film. His reason for being an atheist? He's never seen any evidence supporting the idea that there's a god. He remains an atheist even after meeting an ancient Babylonian deity (which he had a hand in banishing at that).
A recent internet meme from The Avengers. Iron Man: Met two gods, still an atheist. Captain America: Met two gods, still a Christian. Hulk: Met two gods. Kicked the crap out of both of them.
In this article (plus a few others) columnist Damon Linker calls this type of atheism "honest atheism," and is of the opinion that atheism is incompatible with happiness and optimism, and that atheists who exhibit said qualities (i.e. are not Hollywood Atheists) do so inconsistently with their worldview. As one could imagine, many were quick to disagree.
Of the two major atheist characters in Dan Brown's Angels and Demons (a book exploring the concept of conflict between science and religion), one is a bitter, resentful scientist who became crippled as a result of his religious fanatic parents denying him treatment that could have prevented it, who has no sense of wonder regarding nature, the other is a brutal assassin. The former is a borderline case of research failure because a sense of wonder regarding nature is one reason many (if not most) scientists choose the career. However, to balance things out the real Big Bad is the apparently progressive camerlengo who turns out to be a crazed Knight Templar who murdered the Pope when he discovered the Pope had fathered a child. He orchestrated the entire plot with the objective of discrediting science, restoring the world's faith in religion and setting himself up as the new Pope/Messiah. It partially works, too.
Subverted in The Way of Kings. POV character Shallan expects Jasnah, a famous atheist scholar she's seeking out an apprenticeship under, will be this, but while Jasnah's a bit of an Insufferable Genius, she turns out to be overall a likable, charismatic person and one of the smartest people in the novel. At the end of the book, it's revealed that the setting does, in fact, have a god, but he's dead.
In Dean Koontz's Frankenstein we are regularly informed that since Frankenstein doesn't believe in any god, this means he has no reason to follow any moral code. Dean Koontz also wrote a short story called "Twilight of the Dawn" which feature a stereotyped atheist. Victor's lack of morals are also based after his own arrogance and belief that he is the pinacle of human potential. Interestingly Dean Koontz himself was at one point in his life an atheist and wrote a few sci-fi stories dealing with characters attempting to find and kill a God, who is evil.
The Misfit, from short story "A Good Man is Hard to Find," is practically the archetypal dangerous, nihilistic atheist. He decided at an early age that if Jesus never died on the cross, then there's no reason to do anything at all but enjoy himself the only way he knew how: killing. The story may have been a reaction to the rise of existentialism in literature.
Good Country People features the protagonist as a grumpy atheist, who mainly does it solely to annoy people, attempting to "convert" (read: seduce, then crush his beliefs) a seemingly wholesome Southern boy who's got the fire of Jesus in him, selling Bibles for a living. It turns out the Southern boy is much, much more atheistic than her, and is a nihilist who steals disabled peoples' prosthetics For the Evulz. Like the protagonist's fake leg.
Another one of her stories, "The Lame Shall Enter First" features a more positive, humanistic atheist faced with a cloven-footed character who claims to be a Satanist. The Satanist comes across as the wiser of the two: at least he knows how the battle lines are drawn.
Another (kind of) positive portrayal of an atheist (sort of) is the title character from Parker's Back, although he's more agnostic - being vaguely spiritual but not believing in gods and basically treating tattoos as his religion. He's married to a shrewish hateful Christian woman who hates things that aren't Christian and if she hates something it isn't Christian. Also, she falls into heresy. It isn't clear if it's Arianism—denying that Jesus is fully God—or Docetism—denying that He is fully human, but one or the other.
The novel The Last Templar features a character who vowed to destroy Christianity after taking the advice of a priest to not abort his wife's high risk pregnancy, resulting in his wife and unborn child's death. Just to really show he means business, he sets fire to the church with the priest still inside shortly afterwards.
The one-act play "Deus X" plays around with this trope. It concerns a neuroscientist who wonders why he grew up to be an atheist while his brother grew up to be a televangelist. He eventually discovers that religious faith is caused by a gland in people's brains, and develops a drug that eliminates said gland. Although this turns the devout into wanton sex maniacs and the kind of conscienceless people that atheists are often stereotyped as, it is portrayed as unequivocably a good thing, and the play ends with the doctor character encouraging the audience to take a handful of the pills when they leave.
Adam Hauptman of the Mercy Thompson series became an atheist after witnessing the horrors of the Vietnam War and simultaneously surviving a werewolf attack. He's bitter about his memories of dying in the jungle, waiting for God to save him and his comrades. Though it seems his bitterness is more towards his own naivete, he also mocks Mercy for her belief. Mercy herself is shocked that anyone could remain atheist after witnessing the power of Christian symbols to repel vampires and other evil beings.
In the Endworld novels, the Doktor is a prominent example. His devout atheism is due entirely to his parents being killed in a car crash before the war.
The dwarfs in The Chronicles of Narnia by C. S. Lewis stand in for atheists (and possibly Communists). Trumpkin, one of the "good" red dwarfs, helps the good guys in Prince Caspian but denies the existence of Aslan, even when Aslan is standing in front of him (which is how some Christians view atheists as behaving) until Aslan roars in his face. The "bad" black dwarfs in The Last Battle, meanwhile, reject Aslan and are doomed to wallow in their own mortality. Lewis's fiction for adults is actually a bit more subtle than that; there are quite a few examples of this type, but then there's at least one of the True Companions who remains a defiant atheist to the end.
Mackenzie Calhoun from Star Trek New Frontier, who lost his faith in the Xenexian gods after a woman he loved was particularly brutally murdered.
In the 1632 series, there are several characters who are "non-practicing" or "casual" or "inattentive" when it comes to religion, but even then they all have some sense of religion about them and they're generally all nice people. The only character to be flat-out labeled an atheist so far in the series is an actively rude, cynical Jerkass who thinks religious people are all ignorant cretins and doesn't ever hesitate to let them know his opinions about them.
Averted in the Eragon series. The Elves do not believe in or worship gods. Their reason is simply that there is no evidence for them existing and have fun arguing with Dwarves on the matter (who devoutly believe in their god).
In Neal Stephenson's Cryptonomicon, Doug Shaftoe says on finding a sunken submarine, "If anyone was still alive in the bubble, they died a long, slow death. May God have mercy on their souls." Randy Waterhouse surmises that an atheist, confronted with the same situation, would have nothing to say but Yes, the organisms inhabiting that submarine must have lost their higher neural functions over a prolonged period of time and eventually turned into pieces of rotten meat. So what?
In Theatre/RUR, Rossum created artificial humans because he was a materialist, and wanted to prove that God is not needed for the creation of man.
Stannis Baratheon of A Song of Ice and Fire says that he gave up belief of the Seven ever since his parents drowned. Although he takes part in the religion of R'hllor, it's stated that he only does so for the power that Melisandre promises him.
In the Discworld novel Small Gods, Sergeant Simony despises and disbelieves in Om with a fury that is rather impressive, unlike the rest of the Omnians, who have quietly ceased to believe while still claiming they do. Om himself actually likes Simony, whose passion is almost as good as belief. By the end of the novel Simony has actually met Om and becomes more of a Naytheist: "Don't think you can fool me by existing."
Live Action TV
All in the Family: Mike Stivic is agnostic, and is frequently belittled for his beliefs by his father-in-law, Archie Bunker, who — though rarely going to church himself, despite claiming he is a devout Christian — confuses Mike's beliefs for outright atheism. Indeed, in the pilot episode Mike declares there is "no scientific proof" of God's existence, although his actual beliefs in several episodes later in the series reveal he is more agnostic. The perfect case in point was "Edith's Crisis of Faith," where Edith renounces her deep Christian faith after witnessing a deadly robbery; Mike helps her reaffirm her faith by saying God would not want such a horrible thing to happen. Interestingly, Mike also loved Christmas, since the time celebrated the birth of Jesus, to him a kind, wise and benevolent philosopher. As for him the "son of God" part, he called it "ridiculous".
Good Times: Toward the end of the series' fourth season (1976-1977), Michael becomes friends with a strong atheist named Carl Dixon (Moses Gunn), something that irritates Florida. Ironically, by the season finale, Florida and Carl are wed and move to Arizona as a way to explain Esther Rolle's departure from the series (due to her extreme dissatisfaction with the series' turn). Rolle also criticized the way she was being axed off — a devout Christian (Florida) marrying a hardcore atheist (Carl), and when she returned to the show a year later, the producers agreed to her wish that Carl be retconned from the show.
Blossom: Although no episode focused on religion, the Russo family's lack of religion does make it into several scripts. In one episode, where Nick is dating Sharon Lemure, he remarks that — after noting all the historical conflicts based on religion — only atheists seem to be truly happy and at peace.
Lindsay Weir from Freaks and Geeks is an atheist simply because in her view there is no rational reason to believe in god(s), though her atheism is also explained in the first episode as a reaction to seeing her grandmother die and hearing her say how there was no light and she was alone.
Jane Christie from the Britcom Coupling. In one episode she goes to a Christian group and says, "Andrew, lovely! Well, Andrew, there's something I probably better explain. God is just a made up person. You can't expect Him to be answering your prayers if He's not real, can you? That's a bit like writing to the characters of a soap opera and expecting a reply, Mr. Silly Sausage." After being told that the group believes in one true god, she then goes on to state that they should have checked that they have different Gods in different countries. She then wonders if the various Gods are like M Psnote for American readers this refers to a member of parliament, similar to Congressman that they have a different God for each area. Commenting that Thor would be the best head God due to being a muscular blonde who can control the weather.
Admiral Adama, a humanist who views mankind as flawed but inherently good, and ultimately accountable to nobody but themselves for their mistakes in life. While Adama explicitly states a few times that he's an atheist, he sees no problem with using humanity's faith as a rallying cry (such as in the infamous "So say we all!" scene) and accepting some of Roslin's more irrational endeavors (though he's opposed to them early on and nearly topples her government over it). He comes off as more of a pragmatist - seeming to accept that faith is necessary for people to have even though he doesn't share it himself.
Gaius Baltar, an egocentrist who ultimately comes to consider himselfa god (or at least, a prophet). Baltar thinks of himself as an instrument of God (incidentally, the Big G hates it when you call Him that)- he was an atheist, but begins to believe there is something in "Hand of God"- with the apt final shot of the episode.
The Cylon Brother Cavil/Number One Model, the only model to reject both the Cylon god and the Lords of Kobol, and the most sadistic and genocidal Cylon model to boot. While Cavil doesn't believe in God, he has no problem with using "God's will" and the "divine plan" to justify a grand agenda which turns out to be based on little more than petty vengeance.
In a deleted scene we find out that Billy Keikeya was also an atheist, despite being Laura Roslin's aide and most devoted supporter. By then Roslin was having prophetic visions and some people thought she was the messiah; Billy didn't believe in the gods, but he believed in Roslin. Though both scenes which were shot featuring Billy explicitly "confessing" his atheism to Roslin were deleted, you can still pick it up by observing his actions through the show (it's easier to see it once you've been told Billy is an atheist). It's mostly non-verbal - you see him sort of staring down and looking a little ashamed whenever Roslin rambles about Pythia, and in a couple of his scenes with Dualla, she implies her faith and he awkwardly changes the subject, his facial expression stuck somewhere between tolerance and pity.
Gaeta's atheism is presented matter-of-factly, if mostly by implication: he has trouble taking Roslin's 'visions' seriously, and acknowledges to Adama at one point that he is 'not a man to look for religious explanations' of natural events, however convenient those events might be. His lack of faith in any gods is not considered a problem by other characters at any point.
Bones has Temperance Brennan, who argues with Seeley Booth (a strong Catholic) all the time about his faith and her lack of it. This is strong because they both make good points, and neither is instantly converted to the other's viewpoint. She is probably one of the most well-treated atheists on television. She frequently states her rationale for why she doesn't believe in a God in a calm manner - unsurprising, considering she's an anthropologist above all else - and nothing has ever been made of her being "wrong". She and her Catholic FBI partner get into frequent arguments over her atheism, but over the seasons, he's come to tease her affectionately over it. The arguments usually aren't "over Brennan's atheism", though. They're usually started because she'll occasionally come close to picking a fight with him over some aspect of his belief. This stands in contrast to how she's shown to not only be knowledgeable but openly respectful of pretty much every religion but the Jesus-as-savior ones. She tones it down later as she seems to realize she's antagonizing Booth for no particular reason, and it's entirely possible there's a Freudian Excuse for why she has issues with Catholicism. In early episodes, it is clear that Brennan chafes at the idea of faith as being in opposition to reason. Over the years she herself starts demonstrating faith, specifically in her partnership with Booth. This character development came to a head in the 8th season finale "The Secret in the Siege". After Brennan proposed to Booth, and he subsequently broke off their engagement (in response to serial killer Pelant's Sadistic Choice), Booth and Brennan's relationship seemed to be in serious trouble. At the end of the 9th season premiere "The Secret In the Proposal", Brennan assured Booth that she still had absolute faith in him and believed that he would make things right between them.
Dexter Morgan from the Showtime series Dexter, a vigilante serial killer traumatized as a child by witnessing the murder of his mother. In Darkly Dreaming Dexter, the novel on which the show is based, his brother Brian is also an atheist for the same reason. Though it is also implied (at least in the Showtime series) that, rather than actively disbelieving in a god, Dexter simply has no use for religion/the concept of a god.
Patrick Jane from The Mentalist fits the description to a tee. His wife and daughter were murdered and he will mock religious beliefs or any belief in the supernatural, although he may have been an atheist before since he was a secretly fake psychic before the murders. In fact, this is what got his family killed, so it explains his hostility to such beliefs. And when another psychic "successfully" guesses a few things and tells him about the murders, he breaks down defeated and crying. One of the few times he openly wavers on the issue is the episode that ends with Jane and his brother visiting Jane's wife's grave. His brother asks if he thinks she can see them. After a long moment, Jane whispers very softly, "Maybe."
Inverted in Moonlighting. The snarky, somewhat dark, cynic David is a devout believer in God, while his life-affirming, successful partner from a good, loving family, Maddie, is an atheist.
The title character is an utterly cynical curmudgeon, Straw Nihilist atheist as well as a bitter drug addict. Dr. House is actually a more benevolent example than most. In a few more reflective moments, he explains that in the absence of definitive proof one way or another, a belief for or against God is ultimately a choice between what gives more comfort. He simply finds it more comforting to think that existence isn't a test.
His subordinate Doctor Cameron, however, is very idealistic despite being at least nominally an agnostic (she thinks God might or might not exist, but either way she doesn't believe He takes an interest in humanity). More accurately, she believes that whether there's actually a God or not is immaterial, since humanity could never hope to understand him in any case. "I think penguins may as well speculate about quantum physics," as she puts it.
One episode featured a priest who called himself atheist but really had a textbook example of "God did me wrong" Hollywood atheism. Seeing Jesus floating in front of him does nothing but make him check himself into the hospital for hallucinations. By the end of the episode, he had found faith again because the wrong was made right and he made peace with the person who had hurt him.
House's ex-girlfriend Stacy is also an atheist, although she wears a cross she inherited from her mother (atheists can do things for sentimental reasons, after all). It's subtly implied that her husband Mark is religious to some degree; at least, while House is trying to anger Mark, he inquires about their wedding day and gets in a jab about "the atheistical bride".
Mal Reynolds lost his faith in God after the events of Serenity Valley convinced him that God disagreed with him politically. He will allow a preacher on board his ship, but he prefers that he keep his religion to himself: "You're welcome aboard my ship. God ain't." This is called back in The Movie. While Book never tries to get Mal to believe in God, he tries try to get him to believe in something. "I don't care what you believe in, just believe." And he does eventually believe in something: his crew, and that he has to fight for what's right. There is an Alternate Character Interpretation that has Mal believing in God, and just really not liking God at all. This interpretation is shared by Nathan Fillion, the actor who played Mal.
River is also known to lampoon religion on several occasions (albeit unintentionally, she's not looking to cause trouble), most notably when she begins "revising" Shepard Book's Bible to be more congruous with reality.
River: Noah's Ark is a problem. We'll have to call it an early quantum state phenomenon. Only way to fit 5,000 species of mammal on the same boat.
River appears to be a subversion of the stereotypical Hollywood atheist, as her atheistic stance is scientific. She's influenced by the noted inconsistencies she found in Shepherd Book's explanations and the lack of any evidence for religion. She does understand the power of faith and religion though, she just wants it to make sense and be logically consistent (hence trying to "fix" the bible) and her apology afterwards
"I'm sorry, I tore the pages out of your symbol and they just turned back into paper…"
Jack McCoy is an admitted lapsed Catholic. His disdain for religion (or for what he sees as religious hypocrisies) puts him squarely in the "exists to belittle the religious" category, often to the point where he's jeopardized a case just to get his shots in. In the show's defense, he's almost always called out on it. It should be noted that in one episode, McCoy fully considered himself a Catholic and suffered from religious conflict when trying to get a confession to a priest (albeit not a Catholic one) by a criminal while the criminal was in jail admitted in court. Which means McCoy may have been just given a Faith Heel Turn just for the sake of repeated anvil droppings.
Detective Mike Logan falls into the same category as McCoy, plus he's given the Freudian Excuse of an abusive childhood during which he was beaten by his Bible-thumping mother and molested by a Catholic priestnote Unsuccessfully, due to his having been a pretty savvy kid, but some of his friends weren't so lucky.. Before McCoy was brought onboard, if the show was about a religious issue, Logan would be the one to make disdainful and mocking comments about religion and spirituality in general.
The villain of an episode, a European psychologist who tried to instill gender roles in a young sex-reassignment surgery patient through questionable techniques, claimed the religious backwardness of the protagonists' American culture was why they were disgusted by his "scientific progress". It's worth noting that this is based on something that actually happened (save for the doctor being a Straw European or Straw Atheist).
Benson is an atheist, in marked contrast to Stabler, who is Catholic. Benson questions Stabler's belief, arguing that no one could believe in God after all they see in their line of work.
Sam Tyler, the lead character of the US version of Life On Mars, is a lapsed Catholic of the Cynicism Catalyst variety: he left the church after his prayers failed to stop his father from walking out on his family. (The original UK version only briefly mentioned Sam's religious beliefs; he described himself as, 'not what you'd call a religious man.') Although he does seem to take the faith back up for at least one episode after meeting/having a vision of someone that might be an angel/God who lets him see the funeral of his surrogate father and takes a dead little girl to heaven. It's that kind of show.
Perry Cox from Scrubs. In one episode it is revealed that his lack of religion has driven a wedge between him and his fundamentalist Christian sister. It is also revealed in that episode the reason for his atheism is that they were both abused by his father. This was contrasted to his sister's way of dealing, converting to Christianity. It was however later revealed that it was not religion that drove a wedge between him and his sister, but the fact that Cox didn't want to deal with anything from his childhood, and religion was just an excuse. He still does not particularly like religion, stating that prayer gives patients false hope. A talk with J.D. does reveal that he doesn't genuinely begrudge people for their religious beliefs.
Matt Albie from Studio 60 on the Sunset Strip. As one character puts it, "No one delights in tweaking the religious community nearly as much as Matt does."
Scully: You've always said that you want to believe. But believe in what Mulder? If this is the truth that you've been looking for then what is left to believe in?
Mulder: I want to believe that the dead are not lost to us. That they speak to us as part of something greater than us - greater than any alien force. And if you and I are powerless now, I want to believe that if we listen to what's speaking, it can give us the power to save ourselves.
Scully: Then we believe the same thing.
An episode of Red Dwarf features the eponymous Inquisitor, a droid which, after concluding there was no God, appointed himself judge over mortals, killing people to free up lives he feels could be better allocated to those who weren't born. Interestingly, the Inquisitor's 'duty' is based on the notion that life is extremely precious, a common belief in many real atheists. This would make him a Well-Intentioned Hollywood Atheist.
In Father Ted, Father Dougal McGuire is shown in a number of episodes to have no belief in God or any other aspect of the Catholic faith. At one point he discusses the matter with a bishop having a crisis of faith, who ends up resigning his post and becoming a hippie. Of course, he wasn't trying to encourage him to leave the clergy. But this is Dougal we're talking about.
Ted: Dougal, how exactly did you become a priest? Was it a "collect 10 crisp packets and become a priest" promotion?
An episode of the Alien Nation TV series had alien George and human Matt investigating a series of murders among the binnaum, who are loosely the clergy of the Tenctonese aliens (they also play a role in Tenctonese reproduction). Matt remarks he's a lapsed Catholic who left the church because of its hypocrisy. After the events of the episode, the final scene has him walking into a Catholic Church to attend Mass.
In "Grilled Cheesus" with Sue and Kurt: while Kurt expresses dislike of religious institutions because of what he considers their sexist, homophobic and anti-science attitudes, the arguments he uses in his conversations with the other Gleeks about god and faith are mostly the same as those used by intellectual atheists, including Russell's teapot and a brief reference to the Flying Spaghetti Monster. It's also implied that his atheism is of long standing - his speech about his mother's funeral makes it clear that even as an eight-year-old he had no belief in any sort of after life.
Sue, on the other hand comes off as mostly angry at God for giving her sister Down syndrome and tries to stop the students from singing about their religious beliefs - though to be fair, this is also at least partly because their insistence on doing so is causing Kurt, whose father is in a coma after a serious heart attack at this point, considerable stress. Even better, while they both make their peace with the religious (or bow to religious privilege), neither is converted by the end of the episode.
Meanwhile, Finn sings a song about losing faith and the episode treated it in a very cool manner. It's still rare to find a show that's not afraid of sending the message "some people lose their faith; that's ok". Finn's emotional distress at losing his faith in his Grilled Cheesus is not in itself made light of. It's just presented as the logical consequence of a certain rather shallow and opportunistic sort of faith being challenged. The editing of the song sequence does, however, imply that Finn thinks Kurt, as an atheist, feels the same confusion and isolation Finn is experiencing all the time - while making it clear that actually, Kurt doesn't, and that his sympathy for Finn's situation is, for various reasons, not great.
In the Christmas episode "Comparative Religion" we learn that Britta is an atheist and Jeff's agnostic, but neither is particularly bitter or obnoxious about it. Both go out of their way to politely accommodate Shirley's overtly Christian holiday plans, and Shirley's actually the more obnoxious when it comes to other people's beliefs here. As the series has progressed, however, Britta has gotten a bit more in-your-face about her atheism, especially when mixing it up with Shirley.
The clash between this trope and The Fundamentalist was played with in Studies in Modern Movement. After Shirley insinuates that Britta doesn't have a moral code because of her lack of religion, Britta picks up a hitchhiker specifically to show the opposite. This backfires on Britta when the hitchhiker is himself a staunch Christian. It then backfires on Shirley when he's also a big supporter of legalizing weed, and believes himself to be Jesus. They finally come together with the reveal that he's incredibly racist and doesn't think blacks and white should mix. Oh, and he drinks human blood.
On Supernatural, Dean used to be an atheist, at least until he met Castiel and other angels. Now his believing in god is rather pragmatic, not really motivated by faith. Supernatural is interesting in the regard that atheism seemed only to apply to the Christian god. A couple of Monsters of the Week were, in fact, pagan gods.
Played pretty straight with Morgan—he has a lot of pent up rage at religion due to God not rescuing him from his childhood trauma despite his prayers. However, while the character arc does end with him in church, this seems to be more a matter of making his peace with religion than actually becoming religious, as he still doesn't seem to believe in God. In terms of other characters, Rossi is Catholic, Hotch is an agnostic, Gideon has described himself as a man of (unspecified) faith, and Reid describes himself as a "man of science"—though he did have a near-death-experience, and has been rather confused on the matter since then. The show itself seems to be actively agnostic — not in the sense of ignoring the question, but in the sense of very deliberately bringing it up and very deliberately refusing to answer it.
"The Popular Kids" presents the killer as a Nietzsche-quoting teenager who murdered jocks in fake Satanic rituals, blaming the deeply religious town. In particular, he framed a local "Satanic" (read, "atheistic, heavy-metal-listening, and bitter, but not really Satanic or a killer") youth. Reid tells him that, like a lot of people, he's misinterpreted Nietzsche.
CSI: Crime Scene Investigation: Gil Grissom, apparently. When he talks with a Catholic priest he claims that all the suffering caused by religious wars and extremists turned him off religion. Meeting kind and faithful religious people doesn't seem to alter his opinion. Grissom still shows respect toward religion through the series, however; he just doesn't believe in them.
In the Young Hercules episode "The Skeptic", Pythagoras refuses to believe in the gods, saying everything can be explained by science and logic. An annoyed Strife appears and demonstrates his powers, but Pythagoras dismisses them as magic tricks. He explains to Hercules that the reason he doesn't believe is that his father devoted his life to the gods, to the point that he spent more time at the temples instead of with his family. None of his father's prayers were answered and Pythagoras never saw any evidence of the divine beings his father constantly preached about. At the end of the episode, Pythagoras reluctantly admits that there may be beings that seem to be gods.
The Good Wife: Averted for Alicia, who while mentioning she's an atheist in one episode, isn't otherwise shown to be a worse person for it. In fact, although her daughter Grace is a born-again Christian, these different beliefs never affect their relationship.
Played with in Veronica Mars. After a bus driver apparently commits suicide by driving his bus (full of kids) off a cliff, his last acts come under scrutiny. Specifically, when he stopped at a convenience store shortly before his end, he bought a number of things, including a cheap little Christian keychain, which he then shrugged and tossed in the trash. Everyone assumed that this was a sign he was turning his back on God, and planning to commit suicide. When Veronica investigates, she finds that the store has a large sign proclaiming "NO CHANGE (don't even ask!)." So he was just buying the cheapest thing he could to make change, and threw it away because it was a cheap little keychain that wasn't worth keeping. It is eventually discovered that he didn't actually commit suicide; there was a bomb on the bus. Though in fairness, the fact that he left a note saying he was leaving his wife for another woman, but which was vague enough to be mistaken for a suicide note, really didn't help.
In The Bible, the Amalekites are portrayed as Hollywood Atheists.
Averted in Old Harry's Game with the Professor who is one of the kindest characters in the series and is only in Hell because he is an atheist - he points out that he's hardly his fault for not believing in God if He refused to openly prove his existence, but God is shown to love blind faith. The Professor's wife is very much the same. Played for Laughs as both The Buddha and Nietzsche are in Hell too.
An interesting take on the atheism in a world where most of the gods are flat-out evil. Or, well, they used to. There used to be more chaos gods, including the one who was the God of Atheism. In a world where Gods Need Prayer Badly. So the more you prayed to him, the weaker he got, and the less you worshiped, the stronger he got. He would also try to destroy/wreck the other Chaos Gods' plans, and hoped to destroy all gods, including himself. Unfortunately, this fell out of favor with the writers.
The single group that would seem most like they would be atheists- but aren't- are the Tech Priests. They believe that the greatest show of their love is to cut off bits of their bodies and replace them with machinery. However, they do this because they worship a being they call "The Machine God," or "The Omnissiah."
The Tau are atheists, but believe in something they call "The Greater Good." They do believe in their own intellectual superiority, but they are also cut off from a realm of existence called "The Warp," which is where and how the various gods of the 40K-verse work their power.
In a twist of supreme irony, the man who would become the (literal) God Emperor of Mankind was very much an atheist, as demonstrated in "The Last Church", where he argues with the last priest left on Earth about the merits of faith, using only examples like The Crusades and other religious massacres to make his point. One of his sons betrayed him precisely because his Space Marines worshiped him as a god, when he thought rational thought should replace faith. The Emperor was aware of the Clap Your Hands If You Believe nature of his universe, and wanted to make everyone atheists in order to weaken the gods.
3.0 and 3.5 have the ur-Priest Prestige Class. An ur-Priest is a former devotee of a deity who has since turned away from religion and now undermines divine magic for selfish ends. The class's requirements? Must have had access to 3rd level Divine spells, since lost, and must be evil.
The Planescape campaign setting also had the Athar faction, who's big thing was that they believed the gods weren't really gods, just really, really powerful mortals with huge egos, as evidenced by the fact that the gods could be killed. Like the ur-Priest Prestige Class, they had the ability to muck up divine magic but lacked the "must be evil" restriction on their alignment. They were frequently portrayed as being Jerk Ass characters, however. An interesting twist with the Athar is that more than a few of them weren't actually atheists as we'd see it — they believed in a divinity of sorts, they just didn't agree that the beings generally called gods were really divine. The Athar's leader is a subversion. While most Athar join the faction due to being betrayed or disillusioned from their gods and are generally bitter and angry, Factol Terrance simply woke up one morning and realized that he simply did not have faith in his god any longer, so he left his clerical position and joined the Athar. Terrance is also one of the most stable, sane and generally pleasant leaders of any of the Planescape factions.
In Street Scene, Sam tells Rose that happiness is an illusion just like God is. "Then what's the use of living?" she asks him, and he can't think of any reason why they shouldn't kill themselves. She rightfully calls him out for this.
Dom Juan, by Molière. In it, the eponymous protagonist is portrayed as an atheist, whose mission in life is to dare God to strike him down if he exists. He's a doubter like Thomas of Aquin, hence his libertine ways and his pleasure to break anything sacred out of spite (such as sleeping with nuns, offering indecent money to poor people if they will curse God, etc). Except that in the end, God does send somebody to kick his unbelieving ass in the form of an animated statue of a man he previously killed.
Friedrich Schiller's famous piece "The Robbers"/"Die Räuber" has an atheist antagonist - Franz von Moor - who does not believe in moral values at all. He attempts to murder his own father (The Old Count Moor) and discredit his older brother (Karl von Moor) so he can be Count. When his father does not die - he planned to kill the sick old man by telling him Karl died and let the shock do the rest - he locks him in to starve. When Karl returns and orders his men to burn down the castle and capture Franz, Franz has a long talk with himself and then with a priest about the existence of god and about whether he will be punished for his sins. He reasons logically that he doesn't see evidence for a god, then throws it out of the window and becomes religious out of fear. Before committing suicide.
In the musical Celebration, Potemkin used to be a preacher, but since he found out that God is dead, he's stopped caring about the problems of the world.
The atheist in Scribblenauts has the same sprite as "philosopher", and will run away from God in fear, unless the atheist is armed, in which case he attacks God. This is subverted in the sequel Super Scribblenauts (except for the fact that he now has a goth look); the atheist will cause God to disappear on contact.
IsaacClarke is an atheist, as is revealed in a file only available through replay, as well as in comics released to hype the PrequelDead Space Extraction. Though he shows no signs of bitterness or hostility towards the Unitology faith, he does have a typical Hollywood atheist background; when his father died, his mother embraced Unitology with a fanatic's zeal and wasted all of the money that the family had on attaining ranks in the church, forcing him to attend a lesser college than the prominent engineering academy he originally qualified for.
Tales of the Abyss: Religious fanaticism has more or less wronged several of the primary antagonists in several ways.
Sync was one of two surviving clones of the original Fon Master.
Largo perhaps goes the most in-depth, since his Cynicism Catalyst is actually his dead wife while his daughter was taken away from him to replace the still-born princess Natalia. They were more or less instructed to have a child because the Score predicted that the real Natalia would be stillborn, but Meryl, who is the adoptive daughter of the king, was taken from her mother who committed suicide out of grief.
General Van probably has the most horrifying experience with it at the age of 12 he was hooked up to a machine to amplify his powers and forced to destroy his own home town, because the score said he would, you can understand why he wants to destroy it.
In the wii Survival Horror game Cursed Mountain Frank Simmons is a total intolerant jerkass about the Tibetan religion; this attitude towards their beliefs and rituals (along with not doing them properly or not doing them at all before climbing their sacred mountain) leads to a very, VERY angry goddess and basically starts the plot of the game. Eric Simmons, the protagonist, while more respectful to religion, steadfastedly refuses to accept that there might be a supernatural explanation for what's going on, instead insisting that he's suffering things like hallucinations from lack of oxygen with the desperation of a drowning man clinging to a lifebelt.
In Dragon Age: Origins, Morrigan fills the role of the Hollywood Atheist: She's the only outspoken non-believer in your party and also the closest thing the game has to an 'evil' character with an It's All About Me attitude.
Fire Emblem: Binding Blade: Igrene used to believe in God (a different one than worshiped by St. Elimine's church) until the death of her daughter. She preferred to simply stop believing rather than be angry at the being she'd prayed to for years.
Fire Emblem: Blazing Sword has the minor villain Kenneth, who is called out for his actions by Eliwood who says his actions are unbecoming of a religious man. Kenneth retorts by telling Eliwood there are no gods. It seems weird at first that Eliwood would call him out over religion until you actually see his sprite and fight him: He has the Bishop class and uses powerful holy magic; which at the very least proves you don't need any faith to wield them.
Fire Emblem Awakening has another minor villain leading an attack on a religious shrine with priests and innocent bystanders with no reason other than "gods don't exist because I almost died as a child". Also doubles as Flat Earth Atheist, as gods explicitly do exist and factor heavily into the plot and he might have seen that had he lived to the end of the game.
Dark Lord from Sword of Mana persecutes believers in the Mana Goddess not out of disbelief but from anger that the Mana Clan would not use their powers to save his mother.
Played all over the place in the Assassin's Creed series. The Templars (the villains) were originally formed during the Crusades when ten people found a Piece of Eden, a Lost Technology artifact that contained virtually limitless knowledge, and could also produce illusions and control minds. The Templars came to the conclusion that all the supposed miracles of history were merely charlatans using these artifacts, and decided to conquer the world under the theory that there was no God, no divine plan, and no afterlife. Their enemies, the Assassins, are also implied to be atheists for similar reasons, their creed being "Nothing is true, everything is permitted." But while the Templars use this to mean "If nothing is true, then we are permitted to do whatever we wish," the Assassins use it as "There are no limits, so anything is possible." And finally, it's implied that they're right, and there really is no God or miracles.
Lexx in Alien Dice refuses to believe that a caring and just god would allow anyone to have his crappy life (orphaned, forced to play a game where losing means death or enslavement). Which is a problem for Chel, who's a Baptist.
Danny of Other People's Business fills up the criteria of cynical disposition and crappy life, and even equates atheism to a disillusioned christian.
Joel in Concession is an open atheist who hates religion, going so far as to say it "Suppresses free will and punishes scientific progress" among other things. Whether Immelmann shares Joel's views on religion or not or if it's simply a part of the story is best kept hidden to prevent Flame Bait. Technically Joel is listed as Spiritual/Satanic on the cast page, but he does share many traits with a Hollywood atheist (hating religion, a dead sister, a highly religious abusive father.).
The Tiger Barb from 95 Gallons proves to be one during the Christmas storyline; somewhat amusing, given that he's generally a Satan analogue.
Penelope from Questionable Content was raised by fundamentalist parents, which left her with such a hatred of religion that she nearly broke up with her boyfriend for believing in the soul - not God, mind you, much less the Christian God, just the soul.
Similarly, Leslie from Shortpacked! was also raised by devout Christians who ended up disowning her when she came out as gay. She was left with such an hatred of religion that she almost beats up Historical Jesus due to his "cult" ruining her life despite it being repeatedly pointed out to her that there is next to no similarity between HJ and the white caricature bandied about by the American religious right.
Penny from Goblin Hollow was revealed as the Cynicism Catalyst flavor in the aftermath of her telling off a slick backed Benny Hinn-style preacher. Her best friend killed herself out of depression and in the aftermath of this, she heard a radio preacher reference the death in context of how godless and out of control young people were.
The Aeoneonatrix from the Sporewiki Fiction Universe often think of non-followers of their religion (called "the undedicated") as being this way. On one hand, this seems even more unreasonable than usual, as the entry rite to the religion is selling one's soul to a physical god. On the other hand, it actually makes sense when you consider that their god will torture any soul he owns if the person becomes too evil, meaning that all of their great historical villains actually were undedicated, and it is actually true that a follower of their god could never do any of those things. Then again, this is clearly taken to an unjustified extreme. The undedicated are functionally alienated from society and cannot get jobs, make friends, or live normal lives. Despite the illegality of such discrimination it is highly prominent to the point where it compromises the quality of the undedicated's daily lives.
Brian of Family Guy has stated himself to be an atheist, though he subverts this trope for the most part. While certainly cynical and suffering periods of bitterness, overall he tends to be quite cheerful and relaxed about life. The only occasion where he wasn't willing to live and let live when it came to a Christian was when it was Meg, in an episode where she was driving everyone crazy with her newly acquired born-again Christian beliefs, and made Brian into a social pariah by telling everyone he was an atheist. Yet it was actually the book burning that really pushed Brian over the edge. Of course, the episode also ends with Brian convincing everyone that God cannot be real, or else he would not have made Meg as ugly as she is.
Also played straight in "Jerome Is the New Black," in which Quagmire derides Brian for his arrogant attitude toward religious faith.
The Cleveland Show: Brian was possibly addressed as being this in episode "Hurricane": Cleveland Junior says that he doesn't believe in God, but doesn't consider himself an atheist, since he thinks that atheism is just another religious belief. To make his point, he mentions how much of an insufferable douchebag Brian is about his atheism.
Episode "Religionklok": one of the religions that Murderface tries is atheism. Their church is promptly picketed by agnostics who protest for their right to believe in something that may or may not exist. The protest quickly turns into a bloody riot between both religions.
Toki and Skwisgaar are also atheists, mainly because they are nihilists, but it turns out they don't have just a disbelief in God, but they also don't believe in religion. As in they think religion doesn't exist.
Nathan: You mean you don't believe in God. There is such thing as religion.
Skwisgaar: Well then proves it! Show me a miracles that religion exist.
Nathan: Well, um, you know, there's the bible right there.
Skwisgaar: Well... maybe I reevaluates my lifes.
Daria has explained that she doesn't believe in God because she hasn't seen any evidence, but at the same time hasn't seen any evidence disproving God either. She simply believes you should treat people the way you want to be treated and believe what makes you feel best. This only plays in one or two episodes, so it isn't a big facet of the show. Though Jane suggests that Daria just doesn't want to believe in a higher power because if one exists, it means that there's an actual predestined reason why the two of them are outcasts and idiots run the world, and nothing they do can change that. She then admits that's horribly depressing.
Haley in American Dad! is an atheist just to tick off her ultra-conservative dad, though at one time she was dying of cancer, she made a deal with God that if she got better she would save the orphans who were abused by Roger and Steve. The series also has an interesting example in the episode "Rodger Codger": first Hayley belittles Francine for teaching the catechism to some children. After Roger's apparent death, a priest tells Francine that he won't go to heaven, since heaven is only for humans. Francine becomes extremely disillusioned, and pretty much becomes this trope, with the supposedly atheist Hayley trying to make Francine embrace her faith again, so Francine doesn't stay one for long.
Clay Puppington's father, Arthur, on Moral Orel is this. His wife and son are very religious, but his atheism stems from the fact that his wife, who he used to have a happy marriage with, prayed during the pregnancy of her only surviving child (and didn't smoke, or drink, or go on any rollercoasters, or horsebackriding), believes God is the reason her son survived and now favors Clay over him. Clay's behavior after his wife dies contributes to his atheism as well. This also isn't helped that she died because she was absolutely convinced that God had answered her prayer of "Take me and let my son live" when Clay was simply Faking the Dead. She literally willed herself to death because of her faith.