Okay, so I understand people hate and mistrust mutants due to their superpowers, so they become a marginalized class. But tons of people have superpowers not due to mutations they are born with, whether due to technology, years of study, serums, being part alien, etc. But these superheroes are okay, while mutants are not?
Because non-mutant superheroes' powers won't be passed on to their descendants. Mutants aren't feared because of their powers per se, but because they're perceived as a new, rival species whose powers will let them outcompete and replace humans like we did with the Neanderthals.
Granted, some heroes' powers do get passed on -- Reed and Sue Richards had a son who's a powerful mutant, and Spider-Man passed his powers on to his daughter Mayday in the MC-2 continuity -- but bigotry isn't based on facts and reason, just belief and perception.