During the 19th century, the Polish nationalism developed in a way that emphasized the importance of Roman Catholicism as a cornerstone of Polish identity and history. The centrality of Catholicism to Polish identity was encouraged by both of the major partitioning powers, Prussia and Russia, being strongly Lutheran and Orthodox, respectively.

The Czech Republic, in contrast, did not draw as heavily on religious affiliation in construction of their national identity. One reason for this is that several of the early figures used as symbolic of Czech national identity, especially Jan Hus, were not at all Catholic. Bohemia and Moravia were always had a strong (if decidedly minority) non-Catholic religious presence that shaped the regional character. Additionally, prior to independence in 1918, Czechoslovakia had been under rule by the Catholic Austrian Hapsburgs for the past 300+ years, so Catholicism wasn't a useful differentiator from the "foreign rulers".

There was a thread several years ago about this exact question: https://www.reddit.com/r/AskHistorians/comments/14xxsq/why_does_the_czech_republic_have_so_many_atheists/

Edit: Czechoslovakia declared Independence in 1918, not 1920.

In addition to what's already been said, under Communism (And often in Europe altogether) Protestant countries have had much bigger declines in religious expression in general.

While partly this may be the phenomenon of being "technically/culturally Catholic", wherein someone says they are Catholic but does not often attend church and has little interest in religion outside of occasions, there's also the fact that in Protestant countries the church was under the control of the state.

In Catholicism, there is a wider heirarchy that an individual Catholic is a part of, whereas in Protestantism their religious expression is tied much more heavily to the state. Tony Judt, while I may disagree with him on many things, talks about this very well in his History of Europe After 1945.