Let's be clear: The study itself makes no conclusive claims about the causes of colony collapse disorder. Eban quotes from the paper that the research does not "clearly define" that the virus/fungus combination is "a marker, a cause, or a consequence of CCD." A scientist interviewed by Eban very helpfully offers the metaphor of HIV to describe what's going on with bees. HIV doesn't kill you -- it's the opportunistic infections and diseases that follow HIV's dismantling of a sufferer's immune system that do. In the case of bees, the virus/fungus combo are most likely the follow-on infections that kill off an already weakened hive.
There are still major questions about neonicotinoids, a certain breed of pesticides, and Bayer, a major manufacturer has funded swaths of research that seem to absolve their product. Both pieces are definitely worth a read. They also serve as a major reminder to always read with a skeptic's eye.