I think a lot of people and groups are trying to place a secret meaning to the movies and the X-Men comics that just isn’t there. You can pretty much replace “homosexual” with any group that feels persecuted and it will make sense. That’s because, as others have pointed out, it’s supposed to be all encompassing of people (in general) who are marginalized by being different. Originally, it was written with race in mind since it was written during the Civil Rights movement. But because it’s so general, you can plug in any group and it seems to fit/make sense.
And just because a group has embraced something as being representative of their group, doesn’t mean it was created with the intent of being for that group. For example, the Sister Sledge Song, “We are Family” wasn’t written to be a homosexual anthem, but it was adopted as such. And it also doesn’t mean the song is trying to influence people to be homosexuals. So just because some homosexuals see X-Men as being representative of them, doesn’t mean it was written as such. It might has well been vegans that said it represented them (and plug in the word vegan instead of homosexual and it will still fit.)
And as for the bit about American’s being afraid and intolerance… if I recall, the Soviets joined the Americans’ to kill mutants… so I don’t think it was singling out Americans. It’s just that the main characters are American, the X-Men heroes are American, so most of the plot took place in America.
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