I admit I am not an expert in marketing, but I would think they'd also want to advertise to the audience sitting in the 2D theaters, as some of them may be interested in the 3D aspect for Star Trek, but not the film they're currently seeing in 2D.
I agree -- and that was kind of one of my points. I think there are other ways to advertise the 3D aspect of a movie rather than just through a 3D trailer.
A 2D trailer for the people in 2D theaters is important, also. It can get those people interested in seeing the film. If the studio thinks it's important for those people who didn't see the 3D trailer to to have the 3D aspect advertised to them, then the studio will need to find other ways to "push" the 3D aspect 3D on them. A 3D trailer is not the only way to push the 3D aspect (granted -- it is very a good way).