Thank you, Oilcan for posting the dictionary definition of "metaphor." It made my point exactly. I am not suggesting that individual x-characters are gay, but that the phenomenon of being a mutant is like/analogous to/a metaphor for, the phenomenon of being gay.
Like the various <x-man gay> sites you find on the web, I am further suggesting that this is quite deliberate on the part of the screenwriters, the director, and probably everyone else connected to the project. No, Serious Crayons, I don't think someone tried to slip it in without anyone noticing. The director of the first two films is Brian Singer, openly gay. He would stay on in the series as producer and in other roles, and again to direct in a later X-Man film.
Would I have seen this if I had not been forewarned by QasF? I think so. In the first film, X-Men, I could not have put the opening scenes of the Nazi concentration camp into context until later, but it is in the very language of the screenplay besides the plot line and bits of cinematic business that show off the mutant-as-gay theme. This has to be seen in the context of the films--quoting them here would take them out of context and it would not be as obvious as in the films themselves. I will give one example, however. In a later X-Men film a mutant is coming out to his friends. Someone says, "Why didn't you tell us before?" He replies, "You didn't ask; I didn't tell."
Lastly, straight reviews of the films (google <x-men> without "gay") recognize the films as being about minority groups in general under pressure, but then conclude that the metaphor doesn't really work. Gay-site reviews conclude that the metaphor works very well--only if you make it mutant as gay.