While not perfect allegories for real world minorities, I do believe that the superpowered minority trope does work if done well
While I don’t know how well it works as an allegory for any real life issue, I still think there’s value in stories like the X-men because they ask a more fundamental question of whether it’s ever really ok to be bigoted against someone, regardless of any justifications you can come up with.
While racism is in fact illogical, at the end of the day, different races do in fact visibly look different. While most people today would say that’s a stupid reason to discriminate against someone, it is in fact a reason that someone out there might use to justify their hatred. Mutants just take this concept to a more extreme level. Here we have arguably a better reason to be bigoted, after all, they could blow up my house or kill me if they really wanted to, right? But even if we now have a better, more justified reason to be bigoted, should we? I think these allegorical stories essentially say no, we shouldn’t.
And when I say bigoted here, I mean hatred. I think society and mutants do need to work together to ensure they and everyone around them can live a normal and safe life, just like society and disabled people have done in real life (ie ramps for wheelchairs and braille for the blind). Maybe something like a government mandated school to ensure they learn how to safely use their powers, which obviously Professor x already has, or developing an opt-in inhibitor for mutants who no longer want their powers or are a proven danger to them and those around them. But you shouldn’t hate someone who hasn’t done anything, even if they potentially could. I believe everyone deserves that level of decency.
If I put myself in the shoes of a mutant, even if I know some of my fellow mutants are dangerous, and even if I understand and maybe even sympathize with why some people might hate me for existing, I still would not want to experience hatred from people I’ve done no harm to. And like I said, I don’t know how good of an allegory this really is or if the stories in question handle it very well. I think there are some stories where the X-men are against any and all forms of mutant accommodations from the government to help them co-exist in society, which seems shortsighted to me. But fundamentally as a concept I think these allegorical stories that have superpowered minorities do work on some level.