I just read "A movie lover's plea: Let there be light" on boston.com and it baffled me—not from a technical standpoint, but as a movie-lover and as someone who takes pride in what they do.
It's a relatively simple matter: a large number of cinemas aren't changing out the lens between showing 2D and 3D films. While it doesn't sound like a big deal, it can result in as much as an 85% reduction in the brightness of the image when you show a 2D film through the 3D lens.
Unfortunately, it seems that most studios, cinemas, and suppliers of the projectors are not responding to the allegations, or responding in an evasive manner. The spokesperson for Regal, the largest multiplex operator in the nation, was quoted in the article as saying "Patron response has been overwhelmingly positive toward digital cinema and all of the associated entertainment options provided by this technology." Sure the response to digital projectors has been positive; the picture with digital projectors (when used properly) is incredibly bright and sharp. That wasn't the question, though.
I doubt there's some grand conspiracy. More likely it's laziness that it causing the issue, but man, what a shame.