Great article. I made the same unsettling realization a couple years ago. It hit me when I was pondering why the two other ages of reason: the Italian renaissance and greek antiquity only lasted a short period. It seems reason is not a good reason (heh) for self replication compared to religion. The superior demographic powers of the unreasonables always makes them take over eventually.
Once in a while, the stars align and the atheistic/scientific population gets some prominence but it never lasts.
We see the same debates of reason vs religion in the two other periods. See for example Lucretius' epic poem De Rerum Natura http://en.wikipedia.org/wiki/De_rerum_natura
The debate is futile however as even though the texts may be useful in providing inspiration for a Galileo or two to advance science, it doesn't seem to be enough to counter demographics.
At the time, the catholic church had a reign of terror. Going against religion was considered heresy and sometimes punished by death so it's not a surprise everyone were claiming to be good Christians and doing everything to look like good Christians. However, the Italian renaissance ideals were definitely moving away from Christian dogma and towards a more mechanistic, scientific, humanistic and secular interpretation of the universe.
I find Michaelangelo's sistine chapel representation of god being in the shape of a human brain a good example of the whole situation. They were trying to convey subtle messages so that the pope wouldn't notice. Given that Michaelangelo and Leonardo were pioneers on human dissections, IMO it is unlikely a coincidence. http://www.byui.edu/onlinelearning/courses/hum/202/CreationOfAdamBrain.htm