[The popularity of this post led me to reconsider it, and I think there is a significant inaccuracy that has to be taken into account: the Wars of Religion proper were not wars between Protestants (English revolutions are the exception). However, the fragmentation of Protestantism still occurred, and still would be a strong motivator for a philosophical shift toward non-theological views of the world in Protestant nations, so I think there is still a significant truth in my post.]
The historical debate about the genealogy of modern atheism continues amongst historians and theologians, blaming various figures such as Duns Scotus, Francisco Saurez, the deists, René Descartes, and many others. I don’t doubt that some of these figures may have contributed in one way or another, but I remain persuaded, at least for the moment, that the main culprit is really Martin Luther.
Now, I say this as a convinced Protestant. I agree 100% with Luther’s sola scriptura. But I think it was probably the cause of atheism. To boil it down: Luther raised the possibility of a Christianity not founded on Papal (or at least clerical, in Councils) primacy, but based on the individual scholar/Christian reading the scriptures for themselves. Unfortunately, those who agreed with Luther on this starting point failed to present a unified front on several of the important issues in theology and ethics, with the result of the (in)famous fragmentation of Protestantism. This fragmentation became (at least perceived to be; see below) violent with the Wars of Religion, with the result that philosophers started to look for a grounding for politics and ethics outside of any kind of theology. This led to a distinctively modern kind of foundationalism, which, combined with a judgment that there was no good evidence for Christianity, led to atheism.
Now, I think there are two needed qualifications to this thesis. Firstly, I think William Cavanaugh has at least put a big question mark on the general idea that the Wars of Religion was really about, or fought along the lines of religion. More likely it was about the princes trying to get power, and using religious disputes as a justification for their taking more power. Secondly, I doubt there could be a significant explanation of French atheism apart from the apparent friendliness of Catholicism and royal corruption.
But, nevertheless, I think Protestantism has to take a large part of the blame. Because Protestants were unable to secure unity, the state stepped in to do it for us instead. Theologically, this lines up perfectly with Jesus’ statements in his final discourse in John, at least as a mirror-image of what he wanted: Christ said that the world would come to believe based on the unity and love amongst Christians, and so the lack of those things led to the world doing the opposite.
The sad part, bringing things closer to home, is that this failure shows no signs of improving in the near future (witness Dan’s most recent post).