There was also the enlightenment a few decades earlier.
A lot of folks from that time on probably were closet atheists.
After Darwin more felt they could come out of the closet.
But don't forget there is still a huge stigma attached to being an atheist. Try to run for national office anywhere in the US as an atheist and you'll have a very difficult time of it.
Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.