" Stan Lee got the idea for mutants from the racial issues within the 50's and 60's, but what's funny is that the whole racial-like subject is far from over and yet Marvel still hasn't got the idea how old and ridiculous this has started to become. This is exactly why I stopped caring for the X-men, and it's sad seeing that I was once a fan of the X-men and saw them as a team who steered themselves away from letting the world know  "HEY IM A MUTANT, AND IM PROUD, LOOK AT MY X BUTTON".  ....and putting them all on a island didn't make things any better. "

616 Humans wouldn't like Skrulls thats for sure. Again, racism isn't simple, and a lot of people are conditioned into different types of hatred without really understanding the mechanics behind it. Someone made a funny analogy before that makes some other points, since I believe Wolverine is actually quite a popular mutant in 616. At least there have been various storylines where people have touted him as such. Even Colossus use to have quite a few fans back in the day. Mutants were never universally hated, and that was the great thing about X-Men comics, that two sided realism. Depending on what country you live in, similar lines are still drawn over issues like race and sexuality.  
 
A survey/article released a week or so back, pointed out that more males don't mind as much if a female cheated on them with a female, rather than a man, than females, where the man cheats with a man. I mean, that right there is a strange, potentially revealing insight on how people view lesbianism to gayness. Some mutants may be more hated than others. Where as Wolverine might be cool, old school Marrow or Glob might not be. Remember when Masque made the news as well, and what he did to those people? So many polarizing, highly visible mutants on either side of the fence. Its an interesting dynamic. 
 
I mean, lets not forget, ugly people get discriminated too, this would extend to different mutants. Some are hated for their power? Some their looks and differences? Some because ofd their potential. Mutant hatred, complicated. 

OK, imagine living i the Marvel Universe. You have the Avengers, FF, Hulk, Spiderman, DD, and all rhe other hero in villians. Each balance each other out, and came to exisitence from isolated incidences. They became powered through freak accidents that were random and highly unlikely, and furthermore mostly only to people in positions that no common people would ever find themselves in (such as an astronaut, or genius government scientist). But then there are mutants. They can control your mind.  Or some mutant child can't control their powers and blow people up, hell it can be your child. Mutants bring all sorts of new threats. You never know who's a mutant and who's not. Imagine trying to fly on an airplane in a world with mutants. No one can tell exactly who is a mutant and who is not. No one knows how many there are, nor how many there will be. So basically, we know who the avengers are, the FF, Spiderman, etc. We know how many there are, how they came to be, and what they can do. But no one knows about mutants. So there is fear of the unknown, of the threat of such powerful people that may be destined to wipe out humans. Other powered heroes just came and will go. But mutants will stay. (unless they never retcon HoM hich I highly doubt)

just highlighting the fear aspect that some can

Sure, it'd be nice to see other themes brought up in relation to mutants, but it's not really going to happen. And it's not like that's how things work in real life, either.

Humans don't fear meta-humans because meta-humans don't categorize themselves as a "race" like the mutants do. Mutants consider themselves a different race, going so far as calling themselves "Homo Superior". I could understand why humans would take offense to mutants calling themselves "Superior" to humans when in fact mutants are just genetic anomalies, freaks of nature if you will. Sure they have powers, but they are still freaks of nature brought on by the atomic age in the eyes of Homo Sapiens and should not be categorized as a race..especially not one calling themselves "Homo Superior". I can see why human beings would find resentment in that, but I am against any genocidal acts caused by humans against any people/race no matter the circumstances.

It is time. Mobs with torches and pitch forks is not the way things are done anymore. Groups of people beating up mutants is ridiculous too.

Maybe they are scared cuz mutants were born with these gifts. Most other heroes are accidents (Spiderman). But being born with these awesome powers means that any of us (humans) can be mutants and our children. Maybe the fear of a world where humans all evolve to become mutants is a scary thought.   Just try to put yourself in a the world of  Marvel. It would be pretty scary to be a regular guy in a world with mind readers, guys who shoot nuclear blasts from his eyes, etc. We as humans feel we are the the top species of the world. But with mutants roaming, it would seem the the human's time on the top of the food chain is on bought time.  Other heroes, like FF and Avengers have celebrity status so humans dont fear them. But the X-men are slowly coming into the limelight as others have mentioned. And I think we know that Cyclops will lead a powerful X-men team to rival the FF and Avengers as the premiere super hero team.