Why is it that while reading texts on conflicts in Medieval Europe there are always massive implications that so and so happened because God willed it or such and such people were heathens? Was this truly how people felt in those days? Or is this like a literary device for scholars who were often religious people to explain events that they could not comprehend or rationalize without supernatural elements? This compared to writings on rebellions and wars in other regions like China or ancient Rome. In Roman writing it is generally accepted that it was Rome's place to rule the known world as the center of civilization, thus rationalizing its conquests. In China the explanations of whether or not ill events happened was blamed on the dynasty losing the mandate of heaven, a supernatural divinity coinciding with the morality and competence of the rulers. Neither of these implicate that the people themselves were religious or religiously motivated but this is much more the case in Medieval Europe. Religious wars seems to be much more commonplace and accepted as an explanation to how events took place.
I would contend that there were elements of both sides of the argument in warfare in pre-modern Europe. On the one hand there was a level of belief extant in that period that is almost unimaginable to a modern person. This served as the basis for the mass appeal for events like the crusades and the wars of religion. Moreover events such as the relative ferocity of the wars of religion are hard to reconcile without recourse to religion as a causative factor.
On the other hand you have an entirely valid point. Many rulers cynically used religion as one leaver to control both their own populaces and justify their expansion. A good example of this would be the actions of the French kings regarding the Avignon papacy. By protectingthe Popes in their kingdoms the Kings of France extracted many favors and advantages at a low cost. And their opposition to the eventual return to Rome of the papacy points to a motive other then the purely religious.
However at the end of the day we should be aware of our biases. Even the most religious modern historian has a hard time getting into the mindset of the absolute belief that many in the period experienced. This makes it very easy to dismiss the religious aspect of the period. However equally we should not romanticise the past, the Kings and other powerful people of the period were not any stupider then our current leaders. They were able to make decision that were based on self interest even in religious matters. But my readings indicate to me that as a significant factor in these decision was religion.