There's also the perfectly rational fears people have about mutants. It's not like being a real minority where there is no actual danger being around a black person or a gay person. They're not the racist/homophobic delusions people make them out to be. There is nothing inherently dangerous to them. Strip a white guy and a black guy naked and have them fight, they still break in the same places.
A mutant, on the other hand, can be a danger inherently. Having the ability to randomly blast flames, shoot lightning, send shockwaves with your mind, and merely exist like Glob are all legitimate fears. It's not like there is some testing center around and a crap ton of research into superpowers that would make therapy easy or predict what power you'll get.