Aside from a few pet cats and dogs who hang around while their human parents watch anime, most anime viewers are human. That doesn't mean humans are always the good guys, though. In fact, there are a few anime where humans are evil; some shows include moments that make you question who the real bad guys are.
Slavery is unquestionably terrible, but many humans in One Piece control the merfolk and fishmen in mass numbers. In Tokyo Ghoul, it doesn't matter if ghouls are evil; ghoul hunters seem way too gleeful about their jobs. Humans in The Eccentric Family eat tanuki as a delicacy, though they know tanuki are sentient beings.
But these anime do more than depict the evils of humanity in a fictional setting - they also give us the opportunity to reflect on human behavior in the real world.
Humanity's cruelty toward other species is a major theme of Elfen Lied. The Diclonius are similar to humans, but they possess psychokinetic abilities, including powerful vectors that can act as extra arms. These beings have expert attack skills and can spread the Diclonius virus to humans.
Humans experiment on the Diclonius because of their extraordinary abilities. This is largely why many feel hostile toward humans. They're inherently brutal, and humans merely present a persistent threat.
Humans are far from innocent in the world of Princess Mononoke. Rather than coexist peacefully with the natural world, they pollute the environment and hunt animals to near extinction. The environment fights back, though, by cursing Ashitaka and going ballistic.
Can you completely blame nature and the forest for standing up to humans - the original aggressors?
In Tokyo Ghoul, humanoid ghouls struggle to survive in a world that isn't built with their needs in mind. They eat human flesh to survive. They don't want to, but they can't digest any other food. This diet means they must constantly run from humans who want to destroy them. Both sides have a point: humans don't want to be ghoul food, and ghouls want to nourish themselves and survive.
What makes the humans seem occasionally more evil than ghouls? The ghoul hunters can't differentiate between ghouls who slaughter droves of humans for fun and ghouls who don't kill anyone. Some get food by scavenging for corpses.
Ghoul hunters take pleasure in slaying ghouls of all kinds, even small children.
Many of the characters in Claymore are half-human, half-demon beings created by humans to exterminate youma - demons who eat human flesh. Consequently, humans create beings that are obligated to slaughter its own species. What's more, most humans think Claymores are terrifying, disgusting monsters worthy of scorn.
It's hard to sympathize with the bloodthirsty youma, but it's equally hard to sympathize with humankind.