Outside of the Fantastic Four and the core Avengers, I don't think that there are very many characters with powers that the public really does trust. Spiderman and the Hulk have always been mistrusted, Namor's in the same boat as mutants, really; most people probably don't realize that characters like Daredevil or Luke Cage even have powers, and characters like Dr.Strange are most likely not even known to the general public. That all of these characters exist in the same world, and are viewed as they are, doesn't really seem like an hypocrisy to me.
What sets the X-men apart is that they wear their powers on their sleeve as part of their mandate. Whether it's Storm, Wolverine, or Cyclops' team, the X-men are meant to be a public statement about how mutants should be viewed, to engage public perception. Mutants are the issue, not super heroes. Superheroes can just change their clothes when they aren't saving the world, being a mutant is another thing entirely.
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