I don't really know how it's handled in the comics, movies, or games, but I really didn't think the X-Men cartoon series from the late 80's, early 90's did the whole "human prejudice" thing very well at all. It basically portrayed all humans as mutant-hating bigots for no apparent reason, without giving any real insight into why they felt that way.

However, I don't know if I'd specifically fault the X-Men cartoon for handling things that way since that's the way the issue was almost always handled in TV shows of that era. At least I did get the impression that Magneto was more of an anti-villain than a true villain, which made him somewhat more interesting to me than most cartoon villains of the era.