Some small communities remained Protestant during the Counter-Reformation, and were able to practice openly after the Patent of Toleration was issued by Joseph II. While the believing Czech population has been overwhelmingly Catholic since the Counter-Reformation, there was a movement among patriotically oriented Czechs to leave the Catholic Church after the foundation of Czechoslovakia in 1918. Some joined the newly established Czechoslovak Church, some joined the Evangelical Church of Czech Brethren, which was formed through the consolidation of two existing Protestant denominations, and others joined Eastern Orthodoxy. However, this represented only a small minority of Czechs -- in 1930, 78% of Czechs still declared themselves Roman Catholic. What I think is more significant is the importance of the Hussite legacy and Protestantism to Czech national identity. Protestant heroes like Jan Hus, Jan Žižka, and Jan Amos Komenský were reinterpreted as Czech national heroes. Czech nationalists saw the Czechs as an egalitarian, democratic people -- not like those hierarchical Germans and Austrians. They considered the Hussite movement a manifestation of the Czech national struggle for freedom, and the Counter-Reformation an example of foreign repression. The Roman Catholic Church, in this formulation, was essentially un-Czech -- even if most Czechs were Catholic. This formulation of Czech national identity emerged during the national revival of the nineteenth century and was fostered by the Czechoslovak government during the interwar period. Czech Catholic intellectuals and political figures failed to present a compelling alternative national identity that was not so anticlerical.

Some developments after the Second World War further contributed to the decline of the Catholic Church in the Czech lands. New Czech communities established in the borderland regions from which Germans had been expelled after 1945 lacked the traditional ties that connected them to the church. These regions remain among the least religious in the contemporary Czech Republic. Secondly, the Communist government deliberately attempted to break up the traditional authority of the church in village, persecuting members of the clergy and imposing restrictions on religious practice. Government propaganda drew on the anticlerical tropes that already existed in Czech nationalist discourse. So in this sense, yes, the Thirty Years' War did lay the foundation for Czech irreligion... sort of.

Okay, now some final notes. Questions about Czech atheism come up really frequently, and I'm not totally sure why -- I suppose because the Czech Republic looks like a little atheist island on maps of religiosity in Europe, and because it's a clear contrast with neighboring Poland, where the Catholic Church has been closely linked to national identity. I think it's important to keep a few things in mind. First, the Catholic Church remained an important part of life for a minority of Czechs, especially in some regions, even during the Communist period. Many Czech Catholics continued attending church and sending their children for religious instruction, and there were incidents of direct resistance to the regime's persecution of the church. The first mass demonstration against the Communist regime occurred at a pilgrimage in Velehrad in 1985, when a crowd whistled and openly laughed at party leaders, chanting "We want Holy Mass!" and "Long live John Paul II!" I've mentioned before on AskHistorians something that happened in a village in eastern Moravia in 1949, when locals surrounded and physically attacked a group of police officers that came to question the priest. I brought this up not because it was somehow typical -- it wasn't, but because there's a tendency to write about Czech history and national identity from the perspective of the political and cultural elite, among whom these anticlerical strains have been particularly strong.

Finally, those people described as the Czech atheist majority have declared either "without religious affiliation" or left the space blank on the census form. They are not necessarily atheists, although they may be. Since this is a matter of individual belief rather than institutional affiliation, it's a bit more complicated. This 2010 survey found that 27% of Czechs claimed "not to believe in a God or any spirit or life force," which is high compared to other European countries, but not a majority, while according to this more recent survey, 66% claimed not to believe in God.