I've seen it many times before, and used as a justification for why they want X-Men in their own universe:
"The bigotry/racism towards mutants in the Marvel Universe is illogical in a setting where other superpowered beings exist!"
Yeah, you know what else is illogical? Bigotry in the real world.
People hating on others for just the slightest of differences when we're all human is something that's been ongoing since forever and will be for the foreseeable future. That was the point, it was deliberately made to not make sense from the beginning in order to mirror how real-world bigotry works. I mean, some of the most heinous actions committed in human history were motivated by bigotry, even for the tiniest and superficial of differences.
Also, it's been said there's no real reason this would even happen. Actually, there is a source for why they would hate mutants but not the other superpowered beings:
Mutants are considered to be the next step in the evolutionary process, specifically because they were born with their abilities. They hate and fear them because they feel like mutants are there to replace them, and the amount of mutant supremacists set out to do just that lends credence to the idea. We all know what happened to the Neanderthals.
Meanwhile, the mutates of the world don't have that kind of stigma. A mutate is someone born a baseline human, who got their powers later via a foreign element. In other words, people like the Human Torch, the Wasp, Spider-Man and She-Hulk still represent humankind as a whole, just enhanced, but not evolved. Not a truly justified reason, but that's how they see it, and I can at least see how they come to that conclusion.
I've also seen people say "How would you even know if someone is a mutant or a mutate?". Well, that's actually factored into the universe as well. I've been consistently following the new Spider-Man run, and one instance stuck out to me:
Here's a picture of people at a club running away from Billy, the son of Curt Conners aka the Lizard, because they think he's a mutant for his reptilian appearance. He's not. Billy is a mutate, from the same formula that mutated his dad. They had no way of knowing that, however, and assumed he was "one of the freaks". I'm sure I've seen other instances of this happening in Marvel as well.
Anyways, has the portrayal always been perfect? No. I do wish to see the Avengers being more active in helping the X-Men, who they're supposed to be on good terms with. However, I do not think it's a plot hole, but an intended inconsistency to highlight the nature of racism in the real world, which doesn't adhere to any real logic.
As a whole, I'm very much against the idea of the X-Men being jettisoned to their own universe because it speaks of them as though they were just a disposable offshoot of the Marvel brand. In reality, they're just as much Marvel as the Avengers, Fantastic Four and Spider-Man, and should be treated as such. I mean, come on, separating them but treating them as "equals"? Sounds oddly familiar, and ironic...
Thoughts?