I tend to think that when someone says its a good movie but bad Star Trek, they're looking for a reason not to like the movie.
Personal preferences you see. Sometimes you can appreciate artforms through different lenses. In my casual movie lense STID is a decent film. But in my trek lense STID is a mediocre Trek film, my only expectation for Star Trek is for it to be better and more refined than the rest of the films and series out there.
STID's biggest crime is that it can be lumped quite easily with Iron Man 3, Man of Steel and all the other summer blockbusters out there. These films share a lot of things, just not the titles or the names of characters/locations. So yeah gagomg has a point about STID being a decent movie (when compared to what is out there) but a poor Trek film.