X-Men and the concept of "Analogies"
The interesting thing about any good narrative story is that most can usually be interpreted relative to the reader/viewer's personal experience. That's the power of narrative, its appeal as "modern mythology" as it were.
Stan Lee stated in the introduction to the Marvel Masterworks X-Men #1-10 that he originally created the X-Men because he was tired of thinking of new ways for characters to have superpowers. He felt he'd already stretched the radiation accident thin (the FF, Spidey, Daredevil, the Hulk), superscience had been overused (Ant Man, Iron Man, Captain America), alien/outsiders had been done to death (Superman, Silver Surfer, Inhumans, Namor), and even magic was getting a bit hackneyed (Dr. Strange, Thor). So he decided to just start having humans who were "born different." Problem solved, perpetual source of new characters supplied.
The evolution of humanity is a theme that has been played out repeatedly in Science Fiction since Charles Darwin wrote the Origin of Species. H.G. Wells in "The Time Machine," A.E. Van Voight in "Slan" and so on. The Time Machine had a variant human race called Morlocks, who lived underground (after which a group of mutants in Marvel's comics was named). The Slan from Slan were even characters with extraordinary powers, often telepathic, identifiably "different" but capable of concealing their differences, who were persecuted for their powers.
Now of course, the homosexual analogy can be attached to X-Men. Any genetic distinction that could be given a stigma could have this analogy attached to it. Is "Gattaca" a homosexual analogy because it represents a world where people can be discriminated against based on "inferior genetics?" Maybe it is, but that's not ALL it is.
Yes, the Legacy Virus was inspired by the AIDS virus, maybe...but it could also be interpreted as a cautionary tale on the perils of germ warfare. The plague which was intended to wipe out dangerous mutants took out some of mankind's protectors, and then started affecting humans (it mutated, appropriate in a book about mutants).
So people should feel free to draw their analogies, but to determine that your interpretation is the intent of the creators...well that's just silly. At the very least, do your research and realize that the movie is drawing on a VERY large body of literature that should be referenced. You wouldn't write an article on the parallels in a movie about King Arthur or Greek Myth without researching the source material first, and the same consideration should be given to the X-Men (or any other literary character). A little intellectual honesty is all we're asking for.
And you don't get to skate with "but the source material is only picture books." The X-Men (and related) comics probably have more text alone (accumulated over 40 years of existence) than 99.9% of the "serious literary works" out there. And if you had to describe the scenes...well we won't even go there.