These human characters not only agree that Humans Are The Real Monsters, but think this makes it absolutely justified to slaughter a few innocent humans now and then. They may even desire the destruction of the entire human race—with themselves probably excepted.
Sometimes, they tend to be Strawman Political environmentalists who want to "solve overpopulation" or restore the planet to its "natural" (i.e., non-human) state.
More commonly, they appear during an Alien Invasion or its rough fantasy equivalent, believing in the superiority of the invaders. As such, they probably belong to Les Collaborateurs, and expect to be rewarded with overlordship of the surviving humans. This version of the trope is common in the sci-fi "alien invasion" serial films of the 40s and 50s wherein there was always a human collaborator who never seemed to mind that his actions, if successful, would bring about the destruction of his home and everyone/thing he knows.
Nonhuman characters who believe in the moral bankruptcy of their own species may be presented in equivalent ways, but they tend instead to be the more sympathetic My Species Doth Protest Too Much.
A subtrope of Boomerang Bigot. Compare Nietzsche Wannabe, Transhuman Treachery, Hates Everyone Equally, Hobbes Was Right.
The 2003 anime version's Envy also has this vibe to him, believing that people deserve to be tormented for daring to think that their lives have any real value to them. Needless to say, he's one of the most flat out evil bastards in the series. His boss, Dante adopts this attitude as a pose, but it's really just a cover for her own abhorrent selfishness.
The Gold-Toothed Doctor in the manga and Brotherhood series may count, though his reasons for helping the Homunculi destroy humanity are never really explored.
Trigun's Legato Bluesummers is this, especially in the anime where he's comparatively sane and keeps his dignity. It's unclear whether his primary motivation is whatever he knows of Knives' Start of Darkness, his own crapsack life, the world in general, his complete and utter devotion to a guy who happens to be an Omnicidal Maniac, or just his own personal flavor of crazy. He has his own Tear JerkerStart of Darkness in the manga, where he is much less cool but much more of The Woobie (although a disgustingly evil woobie), but in the anime he is both more mysterious and more emotionally self-sufficient.
Sengoku Youko's protagonist Jinka has expressed his hatred of humanity many times, and has made it a goal to obtain a demon's body.
Hody Jones from One Piece. He hates them so much that wants to do a "Final Solution" on them. Why does he hate them? He grew up around Misanthrope Supremes and absorbed their hatred (which may or may not have been justified) as if it was his own.
Mayor Takeshi Hirokawa from Parasyte, who supports the parasites' natural diet despite being 100% human. His internal monologues even categorise humans as "them".
Ra's Al Ghul, Batman's Really 700 Years Old archvillain, is an insane and immortal eco-terrorist who believes that humanity must be eradicated, or greatly culled, to stop them from ruining the planet.
Poison Ivy, another Batman villain, has similar sentiments.
Mister Freeze likewise sometimes wants to destroy humanity, though in his case it's revenge on the world for how it treated him and his wife.
Saturn Queen, in the most recent reboot of the Legion Of Super-Heroes. With her telepathy giving her a constant look at the underbelly of the human mind, she's become convinced that Humans Are Bastards, and that as such, her own thievery, murder, and attempts at World Domination—and those of her partners, Cosmic King and Lightning Lord—are perfectly okay.
Daniel Plainview in There Will Be Blood. In his own words, "I look at people and see nothing worth liking." His son H.W is the only person he treats with anything resembling affection, and that only lasts so long.
Francesco Dellamorte in Cemetery Man - "I have no time for the living" he states, and on advice from Death, promptly embarks on a murder spree.
Marty and Dana, the surviving protagonists of The Cabin in the Woods have fallen into this role by the end of the film. After being subjected to almost everything that the organizers behind the cabin need to do in order to appease the Old Gods and save humanity- along with a harrowing jaunt through the monster-infested facility- a comination of mortal injuries, psychological trauma and despair-induced apathy leads them to let the the human race get wiped out.
Some humans in David Brin's Uplift cycle have declared themselves clients of various alien races believing them to be humanity's long-lost patrons, and occasionally find themselves in opposition to the "free" humans.
In Tom Clancy's novel Rainbow Six, the Big Bad is a Strawman Political of an environmentalist. Rather than trying to save humanity by saving the environment, he and his cohorts seek to kill off 99% of humanity to "bring back nature".
In Have Space Suit Will Travel, two human traitors aid the alien Wormfaces, who capture, kill and eat humans and eventually plan to conquer the Earth and do the same to everyone.
In The Puppet Masters, there are some human beings who do not have masters riding them, who are so vile that they serve as Fifth Columnists to the masters.
The Peace Brigade from the New Jedi Order series is made of this trope. Though it's not so much that they hate the other inhabitants of the Galaxy as they're simply scared stiff of the Yuuzhan Vong. Their mentality is less "our own race(s) suck" as it is "better them than us!"
Dread from Otherland also counts, as he hates everyone and wants to get painful revenge on the world for its mistreatment of him.
Erostratus by Jean-Paul Sartre attempts to make one of these into an Anti-Villain. He compares his dislike of people to another person's dislike of lobster, albeit much less socially acceptable—and much more futile, since everything he does winds up benefiting humanity. As he puts it, "All my life I have been banging my head against a door that says 'No entry if not a humanist.'"
The Mad Scientist in the Alternate History novel Moon of Ice, by Brad Linaweaver, helps a rogue Nazi conspiracy create a virus that will kill all those without blonde hair and blue eyes (which, as he well knows, includes most Nazis). He turns out to be a Jew driven insane by the discrimination he suffered as a youth, who as a result hates all humanity.
Crake from Oryx and Crake believes humanity to be so deeply and irredeemably flawed that he attempts to exterminate all of it and start all over.
Kallor of The Malazan Book of the Fallen is a spiteful, vicious bastard, who's been The Emperor to a hundred kingdoms, and deliberately run them all into the ground. He feels no remorse for this, since he's convinced that Humans Are Bastards, bullies and Domestic Abusers, and that he's just doing on a grand scale, what everyone else does on a small one. He even manages to make it feel rather personal, a feat in and of itself.
Live Action TV
Baltar of the original Battlestar Galactica. (The version in the reboot is more of an Unwitting Pawn.) He'd been promised leadership over the survivors, but was double-crossed by the Imperious Leader who planned to Kill All Humans!. When the Imperious Leader is killed his successor is willing to compromise if the Colonials accept Cylon rule, so he sends Baltar with a Cylon fleet to convince them one way or the other. Unfortunately the Colonials are no longer willing to trust Baltar or the Cylons for obvious reasons.
The Syndicate from the X-Files may be an example, although their cooperation usually seems to be just a diversion to buy time so that they can come up with a way to stop the colonization and save their own lives when the inevitable happens. The Cigarette Smoking Man certainly qualifies, however, as his part in the conspiracy seems to be fueled by sheer contempt and hatred for humanity.
Cigarette Smoking Man: "Men can never be free, because they are weak, corrupt, worthless, and restless."
In "The Seeds of Doom", insane millionaire Harrison Chase helps the Krynoid wipe out all animal life on the planet after it establishes some sort of psychic link with him. In the end, he considers himself to be a plant.
Luke Rattigan in the The Sontaran Stratagem wants to help the Sontarans wipe out all the humans on earth except for the young and attractive geniuses he plans on having sex with.
This was the angle of Heroes Season Two Big Bad, Takezo Kensai/Adam Monroe, a Highlander Immortal who (after a major falling out over a girl with time-traveling protagonist, Hiro) spent the ages growing to hate humanity more and more until he decided to wipe out 99% of the human race in order to become the hero and savior of the remaining 1% because, well, we humans have wars and stuff.
Blake's 7. Travis helps aliens from Andromeda take control of Star One — the Master Computer that controls the Federation — and insists on pushing the button that will deactivate the minefield and let the aliens in. The aliens openly admit their invasion will lead to the virtual genocide of humanity, and are genuinely curious as to why Travis would help them. Travis appears motivated by a combination of self-loathing and desire for revenge on the Federation which he served loyally for years (losing an eye and hand) only to be given the boot when one of his atrocities his superior had previous downplayed was thrust back into the limelight, so he'd be tried and executed before he could be a witness to what she'd been up to.
Knox of Angel, a cultist who worships the goddess Illyria, has the beliefs of this trope. Talking to Illyria, he criticizes humans for being deceitful bastards, and (as happens often), Illyria is surprised that a human can take a position like identifying against his own race rather than with it. Knox's reply amounts to agreeing that yes, he does identify with demonkind rather than humanity (and he is biologically pure human, and not "part demon" like so many other denizens of the Buffyverse).
Exalted: The Deathlords explicitly scout these kind of people to be exalted as Abyssals. Considering the sorry state of humankind in Creation, the challenge is not finding someone who want to hurl everything into Oblivion, it's finding someone who will do it with an undying zeal.
The Enclave in Fallout 2 and 3. Then again, they don't think of the "mutants" (as in: everyone exposed to some radiation) as real humans.
The goal of Big Bad Zephiel in the sixth Fire Emblem game was to conquer the human kingdoms and bring them under the rule of the dragons. He came to the conclusion after his father attempted to assassinate him that Humans Are Bastards, and needed to be brought to heel by the dragons.
Goldman in The House of the Dead 2 (and 4 with a little less narm) creates zombie outbreaks to try and shrink the human population out of concern for the loyfe cycle.
This is the motivating force of quite a few teams in the Pokemon series.
Team Galactic's ultimate goal is to rid the universe of war and hatred (and "spirit" in Platinum version) by wiping it all out and starting all creation over again.
Team Plasma wants seemingly wants to separate humans from Pokemon completely, but ultimately it's implied that only N really believes it. The rest of it is a front so that Ghetsis could rule the world.
Purple Eyes, the end boss of Pokemon Ranger 3, intends to become immortal, summon Arceus, and use it to wipe out humanity because people infuriate him. Out of all the villains in Pokemon to mess around with legendaries, he's the only one who winds up being taken away to be judged. To give some proportion, Cyrus had enacted his plan to destroy and recreate the universe right underneath where Arceus dwells and the worst he got was taken to a parallel dimension that's easily leavable.
In Final Fantasy VII, Barrett's old friend, Dyne, is shown to be one of these. Filled with psychotic bitter hatred after his town was burned down by the Shinra, he was eventually imprisoned in the Corel Desert. When the party finds him, Barrett asks him why he's doing what he's doing, and he says "I want to destroy everything. The people of this city. The city itself. The whole world... even me."
In Hydrophobia, the villains are a group of terrorists that preach that the only way to solve the world's problems is through genocide, suicide and other crimes against humanity. Their "official" slogan is even "Save the world. Kill yourself."
This was the motto of the Church of Euthanasia (below).
Otani Yoshitsugu in Sengoku Basara is hideously deformed due to leprosy, and turned the revulsion and dislike he suffered from it into an immense dislike for humanity in general. Without exaggeration, he is the most hateful man in the world. His goal in life is to kill all people who inspire hope and make everyone just as despairing and miserable as he is, with the exception of Ishida Mitsunari who Yoshitsugu considers to be the only man in existence more miserable than he.
Dr. Weil in the Mega Man Zero series, who hates all humans for making him banishing him and making him immortal.
Demona in Gargoyles wasn't human until Puck cursed her, but she is certainly misanthropic. During the day, after the curse, she fits the trope perfectly.
Gaz of Invader Zim is one of the only people who realizes that Zim is an alien trying to take over the world, but she really doesn't give a damn. This has led to the popular fanon belief that she fits this trope (and seeing how stupid humans are on this show, it's kind of understandable). As further evidence, she becomes disappointed after a malfunctioning microwave that was supposed to destroy the planet, didn't.
Colonel H. Stinkmeaner of The Boondocks is a bitter old man who managed to subside purely on hatred for the rest of humanity even after going blind at a young age. After he dies he managed to impress even the devil himself (who he calls a "BITCH ASS NYU-KKA" to his face) that he's allowed to go back up to exact vengeance.
Mark Twain was one of these in the last years of his life.
"I am the only man living who understands human nature; God has put me in charge of this branch office; when I retire there will be no-one to take my place. I shall keep on doing my duty, for when I get over on the other side, I shall use my influence to have the human race drowned again, and this time drowned good. No omissions. No Ark.".
Serial killer Carl Panzram: "I wish the entire human race had one neck and I had my hands around it" Which he plagiarized from Caligula: "Would that the Roman people had one throat, that I might slit it!"
Daron Malakian of System of a Down exhibits this. At one point he says to an interviewer "I hate you. I hate everyone. Everyone should die."
Of course this is coming from a very heavy punk rocker, so it may not be in a literal sense.
Some environmentalists actually think that humanity should go extinct, not because they will eventually destroy themselves out of stupidity, but rather they think that the natural environment does and will have a better chance of recovery without them.
Fred Phelps, and the Westboro Baptist Church in general, who believe that humans have condemned themselves either by being gay or by not being sufficiently homophobic. "God Hates The World", anyone?
Byron Hall comes across as one of these because his gaming system FATAL puts an alarming emphasis on murder, rape, racism, and the general inferiority of people who don't agree with him. One review even explicitly compares it to the journals in Se7en, a document attempting to masquerade as the product of a perfectly healthy mind, that by its very existence betrays how fundamentally broken its creator is.