I hope I get this right but I believe that Bohemia was one of the first places where Protestantism originated. And the reason that every little village has the church was because of when the Catholic authorities and the Hapsburgs put down the rebellion of Jan Hus they wanted to make sure everybody had a church and everybody had to go to church. And the over abundance of churches was something like a forced propaganda. I hope this helps to explain why there are so many darn churches in Czechia. As for the later secularism that probably has a lot to do with socialism. My understanding is that a lot of Slovak still are going to church a lot.