A lot of these stories don't make sense in a wider context of superheroes living in the same world.
X-Men would probably be a lot less dumb if it wasn't in a setting with all the other heroes.

Some writers do make it out to be that the world of mutants is mostly just people who aren't really in a position to be actual heroes but are still weird or dangerous, and let that move things (so the X-Men themselves are seen as okay or at least tolerable, but your average rando mutant is considered a freak and should be put down).

but then you have weird shit like somebody talking to the Avengers or whatever and being like "man, I'm so glad you aren't like those creepy X-Men" to Cap or whatever -- I could be misremembering all the details, but the gist is there
which might be an attempt to drive the racial point home, that the specifics of how they have their powers shouldn't matter, but there's a lot of anti-mutant sentiment

it still feels fucked up that the whole thing with the movies means that fucking Iron Man of all heroes ended up more popular than Wolverine though, after decades of absolute X-Men domination