system
Given the following post, respond as if you're commenting on Reddit:
human
[Marvel] why are mutants persecuted but other super powered beings are not?

Like the Fantastic Four or Spiderman.
gpt
Spider-Man has been feared and persecuted.

But to answer your question: Part of it is because mutates, those who got power from outside sources, are largely accidents. They don't tout themselves as the next step in human evolution, they're just there because of bad luck (or good luck, if you wish.)

Part of it is also PR. The Fantastic Four were really the first mutates of the modern age, ignoring the Invaders for now, and they were not only open about themselves, they immediately set to work for the good of humanity. This set the stage for superpowered beings to be admired, or at least tolerated.

Mutants, however, had a different introduction. The first real exposure the public had to mutants were the X-Men, a group of superpowered people in full costumes that tried to be secretive, and Magneto, a vocal mutant who revealed himself to mankind by wrecking a military base.

If the public's fear of mutants had a face, it would be Magneto. Since then, mutants have spent decades fighting with humans mostly powerless to interfere. You had the Brotherhood of Evil Mutants, Magneto's Acolytes, Genosha, Onslaught, and, more recently, the Phoenix Five (Who counted several 'good' mutants among their number!) all undoing any good will the X-Men, X-Factor, and other mutant teams might have earned.

So you have a large group of superpowered people who can show up anywhere, be anyone, might not have control over their abilities, a large majority (from the public's perspective) are either evil or just don't care about human lives or property damage, and a bunch of people, mutants and humans alike, who claim that they're the future of humanity and that the entire human race will be replaced by mutants.

On the other hand, you have mutates like Captain America, Luke Cage, and the Fantastic Four, who are all open about who they are and what they do and don't make any claims of racial superiority.