Well, the bees are also dying off pollinating plants which haven't been modified, so that kind of blows that theory out of the water in one quick brush stroke. The most likely candidate is actually the insecticide "Gaucho" made by Bayer (and other insecticides which have a similar method of action):
Bayer CropScience: Gaucho
These chemicals screw up the nervous system in insects, and causes memory loss, which helps to explain why the bees aren't returning to the nest... getting lost... and also how it spreads throughout the colony since they all feed off the same nectar... the insecticide comes with that nectar and the other bees get sick. They are generally in poor health, which makes them more susceptible to additional illinesses.
As much as people enjoy being scared about GMOs, your link does not propose any mechanism by which it would be killing the bees (and again, bees are dying even on plants that aren't GMO, so... ).
