@BraveHeartedHero: This is just my opinion, so take it with a grain of salt. When you consider humanity here, always at war for dominance (be it for economic, religious, invasion, you name it), humans are far from benevolent. We are a warrior species on par with the predators of the food chain (lions and wolves can also be classified as a warrior species). Because of our advancements, we have some huge egos as well. The prime difference between us and the humans of this other world is we have learned to respect life (overall) and try to learn from our mistakes.
Now in comparison to these evil humans (which is not very common in manga. You get evil groups here and there, sure, but not the entire species. That's a bit new.), they actually have another species entirely to wage war against and dominate. Historically, it would be akin to black slavery: a race no better or worse, but still treated like animals and killed en masse because they are "not like me." This part of history is easily a massive stain on humanity. So seeing these evil humans, I'd say this is what happens when such prejudiced people are in complete power (another difference: our world is composed of many leaders while there's only has one absolute ruler) and able to force their beliefs on others. Doing so during a war is the easiest way to do that. Don't believe me? Look how we treated the Muslims as a whole during Osama bin Laden's time alive...it was bad before, but when 9/11 hit, if you were faithful to Islam, you'd best be hiding where no one could find you.
tldr (I don't blame you): These evil humans are just what happens when the prejudiced take over the world.