"Enlightenment" is such a nice word. It's important to remember that it took time for the various strands of the enlightenment to coalesce. Case in point:
“Every good Prince ought by Gods commandment to punish even by death all such as do seek to seduce the people of God from his true worship.”
- Isaac Newton, c. 1688
However, as the blog post linked above notes, Newton's real target and intent is not entirely straightforward. It's an interesting read.