Announcing that Khan was the villain in the film would have proclaimed precisely that and anyone who had ever heard of Star Trek or had a passing familiarity with it would know 'Eh, more of the same stuff, why should I go see it?' ---at least, that was the logic Paramount, not Abrams, used to guide their promotion of the film.
Thank god Paramount wasn't in charge of The Dark Knight. They would have been afraid to alienate general fans and kept The Joker as a secret. Heath Ledger would have been advertised as a small time mob boss named Blake Stone who wants to take over the underworld.
Hiding Khan was incredibly stupid and the lack of an identifiable villain did hurt the film's potential. I was interested in the film because I'm a Star Trek fan, but to general audiences the trailers must have looked extremely generic. Paramount was afraid of scaring off the general audience, but that's exactly what ended up happening.