It still parallels the real world. Mutants are greeted with such hate, because they are so close to their neighbor. The people next door aren't superheroes. Most mutants aren't. They just want to live their lives, but you hate them because last week he didn't have powers, now he's blowing up ish. The X-Men are the mutants, so they get the hate because of what they represent. The other superheroes, no one cares.Also to add to what you said their are black superheros who deal with real world racism like Luke Cage , Black Panther, Falcon even more so when he became captain america. then there Nighthawk from supreme power and Blue Marvel it really is hard to take the fantasy racism the xmen deal with seriously when you have characters that exist in the same world as they exist in who deal with real world racism. I mean look at blue marvel his backstory was that he had to put a mask and pretend to be white in order not to scare white americans of all powerful blackman.
It's the same as entertainers who dealt with that ish everywhere, but in theit respective fields. We don't like your kind, but you can play here, work here, entertain us...you just can't eat/sleep/loiter here. You see their name and think they're black or Muslim, so you hate them, until you find out they're white...then you made a mistake. Same in reverse, you never seen your neighbor but they have a traditional name, you've accepted gifts from them, the neighbor that youbdo know, brought a plate from new neighbor, with food you ate and loved. Then you find out they're black now you hate them. It's not the why, it's the matter of just knowing that someone is different that sparks the hatred, that justifies the X-World.
Better example, you love this person until you discover they're gay, now it's pitchfork time. Racism and prejudice makes no sense in the real world, so it fits the X-Men fine. Franklin Richards is a member of the F4, so he's loved...until it's known that he is a mutant. I can't wait until a writer tackles that story.