When the great Enlightenment philosopher Diderot was teaching Catherine the Great of Russia, he was confronted by “loutish courtiers [who] burst in on him front of the court and one said, ‘Sir, a + b / z = x. Therefore God exists. Reply!’ According to the report … Diderot was struck speechless.”*
What distinguished Enlightenment philosophers like Diderot and John Locke is that their reasoning was largely secular. From our perspective, this seems entirely reasonable, and it is. But reasonable is itself a capitulation to the importance of "making sense," a subordination to the senses and the sensual impulses and logical conclusions that contradict the old authority like scriptures and the church.
As can be seen in Diderot's befuddlement, when systems collide, it is difficult, if not impossible, to reconcile them. Within a social system, we can agree that the systems of religion and science can co-exist, but it is not at all clear how these two systems would either be used to justify or refute the other. Priests declaring that a scientist is wrong about how he's interpreted his data are invariably made to look foolish. Scientists who scoff at the lack of data supporting religious beliefs are faced with a plethora of data about religion's abiding allure. The standards of poetry offer little guidance for solving algebra equations.
I think that it's easy to underestimate the extent to which we're witnessing the emergence of a new social system, one which conflicts with the existing system in so many ways. This is perhaps most starkly and most succinctly seen in the conflict between the ecology and the economy.
* Jacques Barzun, From Dawn to Decadence: 500 Years of Western Cultural Life, 1500 to the Present (New York: HarperCollins, 2000) 373.