Always appreciate your posts, meta. Even the ones I don't entirely agree with, like this one. This post makes me see the brilliance of using the gay metaphor instead of the racial one, as it is a thing that happens on a very personal immediate family level that can (but not always) cause a great deal of stryfe in the family. I think superhuman powers that result in things like death and mind control go a bit more firmly in the  "Oh #$%^, my life as I know it is over!" than the "weird things my kids do" camp. Perhaps the intense KKK-level hatred of offspring shouldn't happen so often, but when your kid starts blowing the roof off and mind controlling you into feeding them candy every day, you don't just say "What's a Justin Bieber," you take extreme precautions, and many families would. And I really don't think we can discount the media's role in shaping public perception of these issues.
I definitely agree that the reactions should run the gamut, but having a large pervasive politically-motivated irrational opposition to a minority group isn't exactly far-fetched. The same can be said on a broader scale about change, too, but change when incarnated, even if only by perception, into a group of people becomes in practice a minority issue. I also think, if they want to comment on how parents treat their children, anti-mutant therapy, drugs especially, would be a much more likely result of mutant paranoia than burning crosses in front of your kids' bedrooms. It would also be a much more likely government safety mandate than 40 foot purple killer robots.
That said, one thing about minority issues that no one talks about is the irrationally positive reaction going the opposite way, the fetishization, the celebrity, applause and envy, even in the face of oppression. I would love to see an X-Men or any metahuman race story deal with that. Add to that the co-opting of mutant-ness without actually wanting to be around mutants. I think that kind of 'outcastness' is far more common today than the picket signs and lynch mobs... of course, that still happens too, but that's a story for another day.