I had this problem with Toy Story 3. 3D flat out makes me puke. Literally. I have horrible motion sickness issues. Cars, trains, planes, boats... oh god boats. Oddly I can ply FPS games 2 inches from my 30" display and have zero problems.
I wanted to see Toy Story 3 but every damned theater whiten a 30 min drive only had it in 3D. It was down right sad. Not to mention the tickets were like through the roof.
I think theaters are ramming 3D down our throats because there is a higher profit margin on them. It costs them pennies to add the support but charge viewers stupid high prices. Higher than they need to be to cover the additional tech cost.