Well, racism and prejudice never make rational sense but yet they never seem to go away. But in the case of attitudes towards mutants within the MU it's pretty easy to understand, actually. Unlike, say, Spider-Man or Thor or Daredevil, mutants are a race whose existence represents a direct threat to the future of human evolution. Mutants literally call themselves Homo-Superior. That's the kind of thing that makes some people uneasy.