Sort of! The X-Men may or may not have been exactly named for Charles Xavier (it varies by canon, there's also the X-gene that causes mutants which also may or may not be named for him) but they are his superhero team and the matching Xs are at least deliberate! I think the M for Magneto is complete coincidence though.

(A lot of movieverse uses Charles/Erik for the ship shorthand, possibly to reduce confusion, but that doesn't really work for the overall ship because the comics kept forgetting what Magneto's real name was and changing it.)