Well, the total number of movie showings in an area are somewhat limited, and don't increase that fast. By splitting the types of experience shown between 2D and 3D, they are reducing the number of showing for people that prefer a certain type of experience compared to if they were all that experience. For people that prefer 2D, this is a reduction in the total showing they could expect, so a loss. Of course it's a gain for those that prefer 3D, and a huge one, since it was effectively nonexistent previously.

What we're really seeing is that people don't like to lose something they had previously, regardless of how small. People who prefer 2D really are having fewer showings available, but the trade-off is choice, and allowing other people to actually experience their preference, which is a good thing.