I especially liked reading about the early scientists who challenged religion's view of the world. Reading about Copernicus, Galileo, and Descartes made me think of the famous Nietzsche quote: "God is dead, we killed him". The ideas presented by Copernicus regarding astronomy really challenged the church's infallibility. The bible has sections which clearly suggest that the earth is still and other planets move around it, and for the bible to be wrong when taken in it's literal translation is a concept that was not tolerated at the time. Galileo was the person who made it so difficult to cast reasonable doubt on Copernicus's theory, as his invention of the telescope allowed people to plainly see and diagram the movement of the planets and ultimately determine, through reason, that the earth was not the center of our galaxy, but actually had an orbit and a spin.
This scientific revolution was, in my opinion, ultimately more important that the protestant reformation or other such challenges to the church, because it's arguments were not against the bible or for another interpretation of it, they had nothing to do with it. They did not even need to address it, only to say that the bible was not necessary to understand the world around you, only your own human faculties of observation and deduction.
I would say that Darwin ultimately dealt the death-blow to the God that had existed up until the scientific revolution. That God had been in charge of everything, however the likes of Galileo, Descartes, and Newton had come and shown that everyday events could be shown to be the result of fundamental scientific principles and not acts of God. So that left God with the sole job of having created everything, including us. Then Darwin comes along and shows that God didn't play a role in that either, and that we evolved (as did every other living thing) also along a set of scientific principles.
From then on, God has had a harder time staying relevant in the world. Today his job description for many people is limited to mostly the spiritual side of human existence and what happens to us after we die. I guess the job market is just tough for everybody right now.