The Mutant/Metahuman relations thing is definately a bit hypocritical; in fact, if I recall correctly, that was part of Onslaught's motives for, well, hating EVERYONE. He seemed to hate mutants because they didn't all rise up collectively and take over, and he hated most superhero metahumans because they were "loved" while mutants, paradoxically, were hated.
Granted, a major difference is in that origin. Most non-mutant superheroes got their powers from some sort of "explainable" circumstance, and things that can be explained are often less unsettling. Whereas with mutants, there is still debate over whether they're the true "evolution" of mankind, or an offshoot (like the Inhumans or the Eternals), depending on the story or editorial mandate. Secondly, most non-mutant heroes acquired their powers through either their own handiwork, or an accident. "Handiwork" heroes in a way include Iron Man or anyone inside a suit or armor, or in some cases "super-soldiers" like Captain America (after all, Steve chose to take the serum, as well as had to undergo training afterwards), or even Dr. Strange. Most heroes tend to fall under the "accident" category, from Spider-Man to the Fantastic Four to Hulk (who is an anti-hero), Daredevil, etc. "Accidental" heroes I would imagine are less threatening because they have that element of, "it could have been anyone", much like those "one in a million" shots like being struck by lightening or winning the lottery. "Handiwork" heroes, you can point to and go, "oh, well, HE made a suit of armor with his genius" or "he trained to be a super-soldier with the military" or "he sold his soul to Mephisto to save his friend" and etc.
Mutants, on the other hand, are born. You're either a mutant or you're not. Not unlike "royals" of ancient times. Complicating matters are the fact that mutants are actually a sort of "genetic minority race" who have some factions that want to dominate the world, or on a lower level are criminals. Caught in the crossfire are those mutants who just want to lead a "normal" life. The X-Men sought to provide both sanctuary and teaching to wayward mutants while at the same time improving mutant/human relations, but their strategy is usually unclear. In some incarnations, the X-Men act as superheroes much like other teams, they simply are obvious mutants trying to prove that not all mutants are bad, but are usually distrusted. Considering that many of the X-Men's dangerous enemies are conncected to them (relation to Xavier, former students/allies, committing acts to specifically lure them or some members our, etc), that muddles matters. Plus, the X-Men also spend long periods of time holed up in the mansion defending themselves from attacks and/or engaging in melodrama, thus allowing some of the more "negative" mutant influence factors more airtime.
Add to all that humanity's fear that mutants will one day overrun the planet and do to them what mankind did to other species of homo sapiens.
The matters that usually got to me was:
1). How the public always seemed to "know" which heroes were mutants and which weren't. In many cases, that becomes impossible to determine unless you know their origins intimately, which isn't the case for a lot of hereos (which is why in USM, the fact that the average citizen thinks Spidey is a mutant is rather accurate). Considering that human/mutant relations are usually so hostile that a mutant is liable to get lynched on the street (or at least have no one call the cops if a big robot attacks them), one would think that any superheroes who didn't publically explain and somehow prove their origin could in theory be mistaken for a mutant (which only happens in some recent titles, like GRAVITY).
2). How mutant/human relations, which usually tend to mirror real life race relations taken to a bit of an Nth level, never evolve or change. It usually just swings from one extreme to another. Some years, mutants are more acceptable, or at least the X-Men are. Some years mutants even have a cultural underground. And others, they're all running for their lives from lynch mobs in masks or Sentinals, and not even the liberal media (who sees any criminal who's not Caucasian as a "victim of society" most times) rises a finger to defend them. No matter how dangerous many mutants are, there'd be some people who wouldn't hate them. Hell, in the real world, dictators with nukes and fetishes for slaughtering peasants have their sympathizers.
3). Non-mutant superheroes frequently team up with the X-Men, or at least don't agree with bigotry towards mutants in general, and yet don't do a damned thing to help them. No speaches by Capt. America, no lectures from the Fantastic Four, no disapproval by Tony Stark or whatever. The only times said things usually happen is if some token "protesters" are outside Avengers Manor because the Maximoff Twins or the Beast are members that month. The X-Men are thus justified in not being terribly trusting of a lot of other heroes; no matter how many team-ups they have, they just don't have their back in the social arena.
Of course, the problem is that the bigotry angle is key to the X-Men, and without it, they simply become a soap opera with powers like most other comics. Plus, the X-Universe is frequently removed from the rest of the Marvel Universe except for crossovers or issues of MTU or a Wolverine guest-shot. Marvel historically "seperated" their universes and rarely had them mingle. The X-books do this, the Spider-books do that, the Fan Four are elsewhere, etc. So a lot of times things that happen in the X-verse don't effect the rest of the MU, and the rest of the MU doesn't usually effect the X-Men. To be fair, in the past few years, whether the stories themselves have been good or not is another matter, but some effort has been made to correct this. Still, until ONSLAUGHT in the mid 90's, the X-Universe rarely ventured into the rest of MU save for lessor crossovers or obligatory fights with other teams (like THE TRIAL OF MAGNETO or something; bet they're regretting taking a few shots for Mags now, eh?).
