To begin with, it really just underscores the absurdity of bigotry.

But one could argue that the mutants have been characterized as bonding together as a with a shared culture. The X-Men keep to themselves in a secretive compound upstate. These dynamics begins to activate "ingroup/outgroup" thinking.

But the most important factor is that Magneto's "evil mutant" terrorist activities are probably all the impetus regular people would need to see any group as "enemies." Ask any Muslim how their life changed on 9/11/2001.

Lastly, we should not overlook the fact that most heroes experience moments or lifetimes of prejudice. Spider-Man was famously on the receiving end of a hate campaign by a major newspaper. And even the most prestigious superteam — the Avengers — have been picketed against.