Originally Posted by
Wiccan
1) Technically, mutants are another race. They're considered an evolution, and so, the "they're gonna end the human race!" aspect of their existence is strong. They were already born that way, while others are actually humans who just got their DNA modified for some reason, and with that, the whole religious thing that the purifiers for example have comes to play. Also, some super heroes don't even have powers, or are just aliens.
2) Anyone could be a mutant. Other superheroes either got on an accident or were given powers for some reason, they're considered this kind of super special rare thing, even if that's not exactly the case. Some of them have secret identities, so they can't suffer from anything in their civilian life where no one thinks they're a superhero, and others are actual politic, military and etc figures, like Captain America, Captain Marvel, any SHIELD agent, etc. But a mutant, anyone on your neighborhood, or your children, or your friends could actually be mutants, either in secret or yet to awaken their powers, and lots of these are just civillians like other people.
3) I mean... Is racism logical at all? Do you think it actually makes complete sense on the real world for black people to suffer from racism? Or for women to not have equal rights? Or LGBT people suffering from homophobia?
4) Mutants are more likely to have weird unusual appearances, like Nightcrawler, Beak, Eye Boy, Bling!, etc, and some of them can't hide it, while most heroes known for the people, like 90% of the Avengers are normal-looking. That's the case with X-Men too, but there's a significant number of civilian mutants and students on the school that aren't like that, and some who don't hide their mutation while super-heroing, like Colossus.