The few reasons I can think of:
1. Prices are stupid. The extra money isn’t for the glasses. In fact, I’m not sure what it’s for. Does the projector cost that much more money to run? I doubt it. The production companies are just stupid. Less people coming to the theater? Let’s jack up the prices! They might be happily traveling down the road that will kill them, especially as Internet movie distribution becomes more prevalent with Internet TVs. But who knows how much money they’re making? Maybe they have nothing to complain about. But, from an audience point of view, $13 or more is just not worth it for seeing a movie one time in a theater. So I think this argument is entirely valid.
2. You get motion sickness. I don’t, but some people do. Obviously you don’t want to watch a movie that makes you sick.
3. The glasses look dorky. I don’t understand this one. They are uncomfortable in their “one-size-fits-all” design. It would be nice to have a pair that are designed more like sunglasses. But if you think you look like a dork in them, that’s just your own self-conscious fault. You’re in a darkened theater. If you’re concerned how you look in a movie theater, you have bigger problems than how you look in a movie theater.
4. Aesthetic reasons. I can only partly understand this. From what I’ve seen, when they convert 2D to 3D, it looks cardboard-cutout-ish and awful. Looks much better if they shoot it in 3D, or if it’s already CGI and they can just move the virtual camera (as long as they do it right; you can’t just move it over a random distance to the side, obviously). Supposedly they’ve gotten better at converting 2D to 3D, but the examples I’ve seen so far have been awful.
I don’t understand the larger argument of a 3D movie in general being bad. The real world is in 3D after all. Do you get mad that a movie isn’t in black and white or isn’t silent?
If you’re distracted by the beauty of the 3D (I do sometimes find myself thinking “ooh, this looks so cool!” especially in a good theater), why is that a bad thing? You could be equally distracted by the beauty of a character, or a set, or the music, or the cinematography, etc. Maybe you will not be as conscious of those other elements because you are more used to them, in which case being distracted by 3D is simply a matter of experience with it. Would you claim that the story is the only part of a movie that is allowed to be beautiful, that is allowed to affect you emotionally?
If it distracts you because you think it is ugly, why do you think it’s ugly? Is it just unconvincing for some reason? As I said, the real world is in 3D and you probably don’t go around with one eye closed because you find 3D ugly. It should make the movie more immersive; from an audience point of view, that’s the entire point of 3D; it makes the world of the film look more tangible. I think that’s awesome, and I hope it doesn’t go away anytime soon. (And I do hope 3D TVs stop using that flicker technology; that’s just annoying. Find a way to get both images up there at once.)