IMO, the safest bet was that Star Trek XI wouldn't get nominated for any major awards. As much as Trekkies may luv the movie and all, I don't think that love extended to the Academy, who still may look at it as being "just another Trek movie" when all is said and done. It really doesn't matter what we think about the movie, because we're not the ones deciding on the nominations.
You can hate on the Academy and call 'em morons or whatever, but to them Star Trek XI was just one of many movies released in 2009 and not some kind of big event they were waiting years for like most of us did. It might have been a different story had it not been for Avatar, which might have "out-Trekked" Trek in the sense that it took audiences (including Academy voters) someplace they hadn't seen before.
Free your mind, and the rest will follow.