Some GM-crops ARE pesticides.
One of them is BT-crops.
They produce BT-toxins that rupture insects stomach.
There is a study that proves BT-crops can kill ladybugs, i don't see how they cant kill honeybees either.
Also greenpeace did a study and found that BT-toxin levels are very unstable in the plants.
What science articles mostly ignore about GM-crops are rogue proteins.

As noted by another response, GMO crops have been modified to include "Bt" genes (aka Bacillus thuringiensis (Bt). Bt is a naturally occurring a spore forming bacterium that produces crystals protein (cry proteins), which are toxic to many species of insects. (see, http://www.bt.ucsd.edu/ for additional information). Bt has been used by organic farmers as a way of controlling insects. The Bt genes have also been incorporated into various GMO crops.

A review of Table 2 and the text of the study appears to show that no Bt was found. Assuming the presence of Bt was tested, it would be reasonable to conclude the GMO crops containing Bt are not problematic. That said, the study is silent on the issue of whether GMO crops containing Bt were present in the study fields. However, other studies conducted by scientists without agenda have indicated that Bt contained within GMO crops and used by organic farmers appears to have no effect on honeybees.

While GMO crops tend to use less pesticides (because they are pest resistant), other GMO crops (aka roundup ready) may promote the increase use of "herbicides." The study found herbicides in 23.6% of samples (pesticides in 100% of samples). Also note, "Within a sample, pollen fungicide loads were significantly higher than loads of herbicides or any of the insecticide categories."

To my knowledge and research, GMO crops and technologies have ignored fungal concerns and do not target fungal infections. Thus, fungicide manufacturers are doing well (see, http://www.farmchemicalsi... for a 2008 industry report)

All of that said, I draw the following conclusions from the article: (1) fungicides are a major problem for Bees that has been overlooked by most studies; (2) GMO crops are not the problem for Bees and because GMO crops tend to promote the use of LESS pesticides, may actually offer a solution; and (3) if I was (I'm not) a producer of GMO seeds, I'm going to start looking at incorporating some fungal retardant genes in my offering.