But alot of villain characters are inhuman looking.  Take the attack on UA for example with villains being portaled in.  A significant portion of those villains were inhuman looking.

There probably is some prejudice and ostracizing, even if its minor, but if you look different or scary, it effects you socially.  Even small differences can have huge impacts.  Just cause different is common doesnt mean people arent people.  An attractive normal looking person would be subtly treated better than someone with scales or made out of sludge.