Xavier and Magneto were a direct allegory to MLK Jr. vs Malcolm X, and general 1960's American racial issues (early comic books involved mutants getting lynched). This was the direct intention of the original writers way back in 60's when it was first written.
Interestingly, the recent X-Men movies don't generally fall into the SFC archetype, at least no more than is required by the nature of the X-Men. Most of the on-screen characters are just "shoots X out of their Y" - Storm, Cyclops, Pyro, Iceman, etc. Of the 3 characters of any gender with any depth at all (Wolverine, Magneto, Rogue), the female is definitely not an SFC.