Ah yes, the good 'ol "humans are racists for no reason in direct contradiction of real life" trope. Seriously, humans are reactionary. Racism comes from seeing inferior development in groups and concluding they must be lesser since advancement of society and technology is what people base such things on (wonder what that makes a primitive society that kidnaps scientists and forces them to invent for it). Also, on behaviors and history. Race is simply a convenient categorization for much, though not all, such situations. Which gets into things like skin color and the like simply being easy identification. There might be literally one person in a million who actually care about someone's appearance in a bigoted way, but it isn't really natural to humans.
So, when it comes to things like beastfolk (or faunus in RWBY) or whatever else in a setting being treated poorly (or allegedly, such as how RWBY shows the inverse of what racism the characters claim), you need to ask yourself "What did they do to earn that treatment?" Because humans, by their inherent nature as a species, aren't going to give a crap about what you look like. They'll only care whether you have anything useful to trade or will be good allies in emergency or war and if you are a threat to the well-being of their people. Well, except for Africa, where genocide is regularly practiced by the indigenous peoples for groups being too light-skinned or too dark-skinned. And Arabia, where the culture and religion teach that raiding and enslaving people, especially sex slaves, is right and moral and will send you to heaven/paradise.
Then again, maybe I'm overthinking it and it's mangaka calling out Japan's extreme xenophobia.