Bambi: The sole sign of human interaction with deer is a gunshot. However, the aversion of this trope is enforced. Walt Disney pointedly refused to make the hunters larger characters because he would have had to show them as two-dimensional villains given their actions.
The Iron Giant is a subversion. A pair of hunters shoot a deer that the titular Iron Giant had been watching, but they are not characterised negatively at all, and the scene is used to show the Iron Giant first learning about the concept of death. Most humans are either flawed but decent or reasonable. To drive the point home, the human protagonist is the Iron Giant's Morality Chain.
In Dumbo, Dumbo's mom was separated from him and chained up in a cage because she gave a bratty human kid a (well-deserved) spanking for harassing Dumbo. This can be a double subversion, however, because from the POV of the humans, the bratty human kid is an audience of the circus, and Mrs. Jumbo's rampage will risk on an injured audience and smears on the circus name, possibly causing it to lose audience and go bankrupt because of the risk of unprotected audience. Even if it's harsh, the Ringmaster was doing what he can to keep the circus alive and allowing animals to have their role in his circus... except that his future treatment to Dumbo is to force him to play the clown and be the subject of further ridicule, thereby the double-subversion.
Cats Don't Dance is a parable in which animals are Paper-Thin Disguise minorities trying to break into show business and humans are the racists of Hollywood, keeping them out. The ending epilogue shows the humans invert this eventually because the animals become movie stars.
Happy Feet has a doubly- Family-Unfriendly Aesop. The penguins think humans are monsters. Fair enough; this is typical for sea creatures. The double-warping comes in the ending, with its giant dance-off. It heavily implies that the only reason the humans are even considering preserving the Antarctic ecosystem is because of its entertainment value.
On the other hand, it seemed a lot of the people in the ensuing montage were using it as political ammunition to put conservation laws in effect they'd already wanted it.
The rats of Ratatouille believe this, exemplified in Remy's father. Remy himself thinks that opinion is rubbish and that the humans are just ignorant, since rats have traditionally been pests, and most of the humans aren't monsters.
The Secret of NIMH is a tough case. On is harsh in its depictions of humans performing animal experimentation on rodents. However, the rodents benefit it from it because they become more like humans. They can read and do math and design buildings and harness electricty. This was the goal of the experiments. The biggest threat to The Protagonist and her family is a farmer whose unaware that an adorable Ill Boy is in his fields.
The Native Americans of the same film are shown in a more sympathetic light, but the titular stallion still doesn't like being trained. The other horses do but they prefer the Native Americans to the Settler.
Finding Nemo takes the misguided point of view. The dentist believes that he has rescued the lame Nemo from the dangers of the reef rather than separating him from his father, and the main antagonist is a slightly hyperactive little girl who doesn't realize that if she shakes the bag too hard she'll kill the little fish inside. It's clearly ignorance rather than malice. Then again, when one of the sharks earlier in the movie hears about Nemo being "kidnapped" he says disgustedly, "Humans. Think they own everything."
Monsters, Inc. is a Played for Laughs version. While the monsters don't show any signs that they consider the human race evil or malevolent, they do consider humans extremely dangerous and go to any lengths necessary to keep themselves safe from them when producing energy from them by scaring children. The basically consider the human race living nuclear power.
The prequel states that monsters think humans are toxic.
Open Season depicts open warfare between a band of beleaguered forest animals and a pack of obnoxious redneck hunters.
Watership Down Holly's flashback to the first warren's destruction but reversed when the farmer's daughter saves Hazel from the farm's cat.
Zig Zagged in Once Upon a Forest. Cornelius, who was caught in a trap when he was younger, warns them about humans and is not surprised when toxic gas devastates the forest. The reason for the toxic gas is a human littering with a glass bottle which blew a hole in a tank trunk. The truck driver, by contrast, has an Oh Crap reaction and runs to get help. At the end of the film, help arrives. Humans in scary Hazmat suits have come in to clean things up, surprising the elder.
Battle for Terra plays with this trope. The Earth is destroyed and what's left of the human race is forced to live in a military fleet which invades the peaceful title planet. While they are doing this by force and goal to the kill all the aliens they are portrayed as simply desperate. If you want to know why don't they just live together, the humans and terrans don't breath the same air. Further played with in that the President and his council are Reasonable Authority Figures who want to explore all options before they go with genocide, but a coup happens with a General who advocates an "us or them" position.
In Aliens, Burke tries to impregnate Ripley with an alien.
Ripley: "I don't know which species is worse. You don't see them fucking each other over for a goddamn percentage."
Alien³ follows as a result of the second, but Company members arrive and try to cash in on the aliens.
In Alien: Resurrection, it's the military that is tinkering with alien genes to create weapons.
Downplayed in Prometheus. The worst humans seen are more selfish and/or pragmatic than anything else and the rest are pretty decent. The alien on the other hand (the Engineer, that is) isn't just a monster; he's the most evil character in the entire franchise. However, this is certainly the view of the Engineers themselves, who seem to believe in something fundamentally wrong with humans that needs to be wiped clean.
James Cameron's Avatar is a perfect example of this trope played with. The human RDA are intruding on Na'vi land and destroy the home of the Omaticaya tribe in order to acquire Unobtainium, and follow a rigid, aggressive schedule for this. On the other hand, the RDA tries to negotiate with the Na'vi, and even when they do attack they try to be "humane" first (i.e. hitting the Na'vi with gas and trying to intimidate them into leaving) and avoid bombing them from orbit because they want to minimize local casualties. Then the gloves come off, RDA destroys Hometree, killing hundreds of Na'vi in the process. When the Na'vi assemble an army for war, the RDA tries to destroy the Tree of Souls to break their spirit. Selfridge, the corporate head of the RDA, reacts to destroying the sacred Na'vi site with the same apathy that one would associate to accidentally swatting a fly, though he does appear significantly more disturbed when they take down Hometree. In fact, he and the other officials look downright horrified at the violence, and go out gracefully at the end, following the Na'vi victory.
In the case of Selfridge, He likely was simply indifferent to the Na'vi, as many real-world humans are to animals, without being malevolent or sadistic. To his point of view, the Hometree was just a tree, albeit one sitting on top of the biggest deposit of Unobtainium in hundreds of miles. As he points out, there's plenty of trees around, and to his narrow way of thinking there was no reason they couldn't just get up and leave.
Quaritch is a standard Colonel Ripper in the end. It seems that after the escape of Jake's gang, Quaritch takes over control at the RDA base, The Plan to destroy the Tree of Souls is his brainchild.
Jake Sully and his gang are a inversion of this trope; showing there are humans who are not only truly sick of the atrocities committed by their corporation, but also actually work to stop it with their own power.
The movie provides quite a disturbing meta-example. Humans in-universe may be unwilling to resort to outright genocide or orbital bombardment, but such suggestions arise in movie reviews and discussions with alarming frequency.
Whenever they find an alien nest in D9, they torch it with a flame thrower and laugh at the popping noises that the alien larvae make as they boil.
They set up a firing range and they shock the main character (who is the only human who can use alien tech) to get him to pull the trigger on the gun they strap him to. Then they bring in a new alien gun and repeat the process many, many times in order to test the effects of each weapon. Cries of "I'll pull it! I'll pull it!" are ignored, and they never once see if he'll keep his word and pull it without the shocks.
The MNU literally uses the aliens as target practice. They test weapons against living aliens to judge their effectiveness.
They spread Blatant Lies about the aliens that most people take at face value. One being that the aliens don't care for their young. They love them just like a mother loves her child Have a poor grasp on the concept of property It has more to do with the fact that most of them are starving, and have a perfectly good grasp of it. Yet another is that as a species they enjoy destroying things (tying into their lack of the notion of property) and cite the fact that a group of them derailed a train, supposedly for fun, as evidence. The alien "Christopher" comments on his blog that in reality the group of aliens were an organized resistance group who derailed the train as an act of sabotage directed against the South African government, which had hired MNU to administer D9, in retaliation for repeated abuse by MNU. Although they started to enjoy it, what with the whole "not telling people why they did this, so people just think they did it for lulz".
Gangs from Nigeria move into D9 to get the alien weapons, for which they trade food to the starving aliens at exorbitant prices, unless they decide to simply take the tech, kill the alien, and then sell the alien's organs as a sort of "herbal remedy" that they claim cures all illnesses. The Leader of the human gangs seems to believe that eating the aliens will one day allow him to use their technology, though he also seems to enjoy it too.
When the human main character starts turning into an alien after a concentrated dose of Applied Phlebotinum, his fellow humans plan to dissect him while alive and conscious in order to learn how to give all humans the ability to use the alien tech (which only activates for the alien's biology, including the main character's hybrid form).
Our main protagonist is the one good one, right? No, he's no more sympathetic to the aliens until he begins mutating. His motivation is more "save my own ass" than "For Great Justice," though he does come to care beyond that as time goes on.
Basically, it's a rare movie whose ending leaves many viewers saying they hope that word gets back to the aliens and they come back and death-ray the crap out of humans.
In the French-Canadian cult TV show Dans une galaxie près de chez vous (In a Galaxy near you), it was already established that earthlings (read: Humans) were Jerkass morons who wrecked their own planet. In the two movies, we see: Plot Device anglophones coming from nowhere threatening to exterminate a tiny civilization of cave-dwellers already terrorized because of the sounds of an underground waterfall, Aliens vomiting at the simple mention of the word "earthling" and a failed Write Back to the Future attempt because of ridicule in the internet. To be fair, the only ones in the crew who never have a Jerkass moment is the dumb-as-rocks pilot and (outside of the reveal episode) the half-alien radar operator (who is played by one of the head writers, and, in later seasons, is dangerously entering in Mary Sue territory) and both like to use the Constantly Backstabbing scientist as a punching bag (like everyone else for that matter).
The major theme of King Kong is that man is the monster.
In the original version of The Day the Earth Stood Still (1951), an alien shows up and tries to give humanity a machine that would allow for interstellar communication. And how do the humans respond? By shooting him. After he recovers he spends some time observing humanity and eventually decides to show he means business by disabling all human technology on the planet (with a few exceptions, he left alone planes in flight, hospitals, and the like) for a short period of time. Then the humans shoot him again, this time killing him. He gets better, scolds them for being so violent, and essentially says that if humanity keeps this up the interstellar community will have no choice to put them down in order to prevent humanity from carrying its warlike ways out into space. Both the original and the remake try to paint human actions as irresponsible, rather than outright evil. See also: Humans Are Morons.
The aliens in It Came from Outer Space (1953) believe humanity's xenophobic response to their hideous form will inevitably lead to conflict, so they attempt to repair their spaceship secretly. Unfortunately their covert actions only increase the belief among the protagonists that the aliens are up to no good. Ironically while both aliens and humans are seen acting out of fear and suspicion, neither side is portrayed as particularly unreasonable or malevolent under the circumstances.
Planet of the Apes: Beware the beast Man, for he is the devil's pawn. Alone among God's primates, he kills for sport, or lust, or greed. Yea, he will murder his brother to possess his brother's land. Let him not breed in great numbers, for he will make a desert of his home and yours. Shun him. Drive him back into his jungle lair, for he is the harbinger of death.
Luckily the later movies even this out, the apes are using Ape Shall Never Kill Ape as an excuse to do as bad to humans (if not worse than) what the humans did to them, and later prove they're just as bad as the humans.
Lampshaded when one ape crosses the Moral Event Horizon, and others find out about it. A human observes that they "just joined the human race."
The reboot trilogy is more even-handed somewhat in the conflict between human and ape characters, but still a lot of the plot is kicked off by the humans being dicks to the apes with very flimsy justification.
That would be Humans Are Morons. The Humans Are The Real Monsters, too, but that's because they opt to fight and kill the aliens who are only trying to warn them about the dangers of creating the "solarbonite bomb."
The Happening, aside from the whole "plants are pissed at us" thing, has a very subtle passing reference to the trope. Right after the unfortunate scene with the lawnmover, the protagonists run past a billboard advertising homes. Set on top of the billboard is a smaller line: "You deserve this!"
Agent Smith in The Matrix gives "The Reason You Suck" Speech to Morpheus in which he claims that humans are more similar to viruses than mammals, because they exploit the world and drain it of all possible resources rather than instinctively seek out a natural equilibrium with their environment.
Except that invasive species are usually introduced into a separate ecosystem by the actions (either consciously or by accident) of humans, while a migration to an entirely new habitat in amounts that are relevant are usually very difficult for a species in the wild. Besides, population dynamics take care of the rest (too many carnivores who nearly extinguish their prey species? Mass extinctions for the carnivores who have nothing to eat, followed by a regeneration of the prey species' numbers, rinse and repeat). There is obviously no instinctive harmony drive in animals but due to the self-regulating nature of ecosystems, there is an overall balance - which humans tend to fuck up. So, while Agent Smith's reasoning is scientifically wrong, the point somewhat stands.
Later, ironically enough, Agent Smith becomes a computer virus in all but name.
This trope is the ultimate nature of George Romero's Living Dead series. The Zombie Apocalypse is, more than anything, a way to provide pressure on the humans, who ultimately turn on each other.
Night of the Living Dead: Faced with walking, flesh-eating, corpses outside, the humans inside are too busy bickering and quarrelling with each other to mount any credible defense. The sole survivor, who makes it through the night only by luck, is promptly shot and nonchalantly dumped on a fire as yet-another zombie by people who can't be bothered to check he's still alive.
Dawn of the Dead: Humans are so quarrelsome and irresponsible that they cannot mount any coordinated offensive against the living dead. The protagonists prefer to mindlessly hole up inside a mall and just let the world go to hell outside.
Day of the Dead: The last remnants of humanity are just animals trapped in a cage. The scientists and civilians just want to drown themselves in hedonism one last time, the military are depicted as psychotic maniacs, and the most sympathetic character is a zombie that has been given some semblance of human intelligence back.
Land of the Dead: Arguably the most Anvilicious of depictions, where one gets the sincere feeling that we're supposed to be rooting for and sympathesing with the zombies.
Diary of the Dead: Awkwardly shoehorns it in as the final comment from a surviving main character.
Survival of the Dead: The most subtle of them all, and could almost be argued as being free from it, except for the fact we once again see a cluster of survivors wiped out because they're too busy squabbling even in the face of a Zombie Apocalypse.
The humans in the film version of Starship Troopers are brainwashed fanatics living in a fascist dystopia moving out into the galaxy and slaughtering the Arachnids for territory to expand into. Then again, in this case the Bugs aren't any better.
In The Return of Hanuman, most of the divine beings in Swarglok wouldn't dare to reincarnate to Earth because in the modern times Earth is dangerous, with dangerous humans. Despite of that, Hanuman still believes that there are nice people remaining on Earth.
Lampshaded by Kermit in The Muppet Musicians of Bremen after he intruduces the four protagonists, the titular animal musicians, and the antgonists, their abusive owners.
Kermit: (to the viewers) "You may have noticed that the heroes in our story are all animals, and the villains are all people. I hope none of you takes that personally."