We don't have any evidence
that the villain isn't
Khan; what we have are public statements by several people who are engaged in part of the production effort to keep the identity of the villain a secret.
And BTW, it's entirely possible that the majority of actors in the film don't know the actual identity of the character that Cumberbatch is playing, either. In some ways actors are the easiest people to keep in the dark about such stuff.
The suggestion that the villain is Khan is not based on a single rumor somewhere, but on several inside sources talking to writers at several websites over some period of time. There is no way of knowing yet just how this will pan out - but then, it sounded fairly outlandish a couple of years before Trek 2009 was released, when Drew McWeeny suggested online that just maybe
Abrams was about to blow up Vulcan.