Having recently purchased the graphic novel reprint of X-Men #1-10, I was thinking along similar lines the other day, but arrived at a slightly different conclusion about the origin and "meaning" of the X-Men.
Stan Lee and Jack Kirby's work did a dramatic change even in the first few issues, as each character underwent a metamorphasis into their more contemporary roles. Beast was initially a Yancy-street gang/Dead-End kid full of 1940's street slang and lingo, but by issue #10 he was erudite and using "two-bit words," as noted by Bobby Drake.
Likewise, Scott Summers was originally called "Slim" Summers, Jean Grey marvelled at her form-fitting costume "as if designed by Christian Dior." The entire dialogue elements of the early issues felt like WW2 comics. Part of this was due to Lee's formulaic reliance on team dynamics and part was his attempt to quickly thumbnail characters by their speech patterns. In the introduction to the graphic novel he even specifically mentions how X-Men was supposed to be a riff off of the Fantastic Four. The Beast was like the rough-spoken Ben Grimm and "Slim" Summers was a facet of Reed Richards. Professor Xavier was probably another aspect of Richards's genius. "If they liked the Human Torch," Stan said in reference to Iceman, "then why not a cold version"
My impression was that the X-men were representative of outsiders trying to fit into the general population, combating stereotyping and prejudice, but in specific, they were analogues for teen angst and the painful process of maturity.
Just on the major student character from the movies, I came up with these comparisons:
Cyclops: The optic beams are the unbridled power of the onset of adolescence. His visor represents the ubiquitous glasses of the nerd-caste. He must wear them constantly because of his physcial "ailment," just as a myopic child has to wear glasses constantly. Even sleep is difficult for Cyclops because his handicap dominates his life.
Iceman: Bobby Drake's role is a small one in the first film, much expanded by the sequel. By the second movie Bobby's encounter with his parents and the revelation of his differences is clearly a homosexual metaphor as has been mentioned by other posters. In the comics, many mutants have to go through this painful process, proclaiming their inherent differences to their parents and trying to adapt to a life of being an outsider.
Rogue: She can't touch or be touched, a classical reference to John Campbell's Virgin-Whore construct. Rogue's desire to be part of humanity, to contact others represents the fear of contact all adolescents go through. Her romantic relationship with Iceman, as underscored by Peter's caricature shows what happens when the pair try to kiss and seal their desires. She is about frustration and desire coupled together.
Jean Grey: Jean is mature and a powerful female figure, but her driving force is the desire she feels pulling her from Scott to Logan; the intellectual versus the hormonal. Ultimately she chooses Scott, because her love for him is based on logic and reason, but her love of Logan isn't lessened, just not acted upon. The unrequited-in-kind love between Logan and Jean is paralleled by the unrequited-in-kind love between Logan and Rogue.
Logan: Wolverine is the epitome of rage, the only greater personification would be the Hulk, but Wolverine is close. How odd Wolverine made his first appearance with the Hulk. Logan's love for Rogue is part of his growth, returning to humanity by extending help to her in the first movie. He was the first to accept her as a mutant; she the first to accept him as a fellow human being. Together they are bonded in this, but the age differences lead to a paternal relationship rather than a more contemporary romantic one. There are undercurrents of romance, as Rogue is coming of age, but nothing overt.
Logan's rage is a metaphor for the hormonal rage of adolescence, the desire to rend and destroy.
Storm: Ororo is the calm and passive female lead, exotic, strong, intelligent - a teacher. When she does become angry, the heavens are at her beck. In many ways, she's the ideal of growth and foreshadows how the other characters hope to be once they fully mature. She is a student and not a teacher, in the movies.
Nightcrawler: Kurt is the outcast, the pariah, an intelligent mind trapped in a bestial form. Loving, caring, gentle, but by all appearances he is a terrifyingly fanged and fork-tailed beast. Almost invisible in the shadows, he dwells outside regular society. A member of the circus, trained as an acrobat, Kurt is the fearful manifestation that we all feel, deep down, as ourselves being side-show freaks.
/ramblings