Remember: Politically and socially, Afghanistan is effectively in the middle ages for the most part. If you went around Bible burning in medieval Europe, I don't think you would last very long. Heck, even in parts of modern America if I went around burning Bibles my life would end rather quickly.
Also, I would be hesitant in assigning the cause of the protests solely to the Quran burning. I mean, we are occupying their country and killing their fellow countrymen. That certainly cannot be fostering good relations. It is more or less the same thing the Russians had to deal with.