This question is based on the premise of the X-Men franchise, where superheroes that pass the potential for powers through heredity are used as a metaphor for persecuted minorities. I find this metaphor is self-contradictory because in real life the differences because skin-tone is cosmetic whereas super-villains potentially constitute an existential threat to the human race.
While I can understand trying to exterminate/brainwash/cure/rehabilitate super-villains, the vast majority of super powered individuals have human emotions and conscience. While they might cause accidental harm due to inexperience, they could potentially profit from their super powers.
Forget military applications, someone with ice powers could open a year-round ski resort in the Bahamas! Even seemingly useless superpowers could be exploited with enough creativity. To say nothing of how useful are mundane powers that make you equal to Einstein or an Olympic athlete.
Are muggles more likely to try exterminating all super people or more likely to exploit them?