Just one of those comic book things you just kinda have to accept.
I love how you just rolled right by like six legitimate, logical responses to the thing you "just kinda have to accept."
Again; you're treating the persona of a mutant in the MU as virtually identical to the persona of a superhero, when the fact is that in reality they are anything but alike. The only thing that they have similar is their powers. A "superhero" has a face, a name, a personality, and often an origin right out there for anyone who cares about it to find out. A mutant does not have that. A mutant is just a random individual in a race of
millions. The way that someone would perceive Ms. Marvel the SHIELD Agent and the way that the same person would perceive Sammy the Squid Boy from Random City, USA is
completely different.
That alone answers at least half the question in itself. Why would people in the MU treat mutants differently than superheroes, you ask? Well, because they are different. It's often just as simple as that. You're comparing the comicbook social equivalent of celebrity law enforcement to an
entire race of beings living in your neighborhood and being born from your children. Even if superheroes face persecution -- and we know that they do, constantly -- it's going to be different from the persecution that mutants face because, again I reiterate, they are not the same thing. A hater might accuse Spider-Man of being a crappy hero or even a troublemaker, but even the most dimwitted civilian doesn't think that Spider-Man is going to turn his child into more Spider-Men. Even the most anti-hero crusader like, oh I dunno,
Jameson doesn't actually think that one day superheroes are going to mass together and usurp the nation. That's simply not a stigma associated with superheroes.