I think you're assuming too much.
Dude, the audience and critics alike would complain that secret societies who dress up in outfits and manipulate events from the shadows belong in James Bond and not in Singer's X-Men. I'm starting to think most fans of the X-Men films are snobby types who are ashamed of the fact that X-Men began as a comic and are contemptuous of the term "Superhero".
Same with "Dark Knight" fans, I mean even Nolan himself sometimes seems like a guy whose ashamed that Batman is a comic character and says stuff like "Dark Knight isn't a superhero film, it's a down-to-earth crime drama!". There's no room for the fantastic with these folks.
Honestly, your argument sounds like a similar sort of "snobbishness", just directed against naturalism in superhero movies.
Speaking as a fan of naturalism in superhero movies, I'd have no problem with the idea of mutants influencing the government and the like. It's just
exodus said, it's all in the execution. If done well (eg X-men 2), it'd be well-received--remember that Stryker, a US Colonel had a massive secret underground base
in Canada, which stretches belief a fair bit if you think about it.

If not done well (eg X-men 3), then the audience will not accept it. I mean, is Magneto lifting the Golden Gate bridge really that much worse than Storm summoning half a dozen tornadoes at once, on the face of it? But people deride the former and at least accept the latter, because the overall presentation of the movies help in that regard.
That said, I'd have no issue with some of the more fantastical elements of comic books in superhero movies
if done right. Even aliens would be acceptable as long as they're portrayed as interesting characters with decent motivations in their own right.