Religion is simply not part of the Czech national identity. In Poland and Slovakia, countries with very similar cultures, for instance, being Catholic is part of being a Pole or a Slovak (even if a lot of these "Catholic" Poles and Slovaks are these days not actually religious in anything but name). But when the idea of the Czech nation was being developed in the 19th century, organized religion just wasn't a part of it. Most of the big events in Czech history that endure in the national consciousness were rebellions against or oppression by religious authority, whether its the Hussite rebellion or Battle of White Mountain (and the execution of the (Protestant) Czech nobility by the Habsburgs). The church has always (since the 15th century at least) been seen as a symbol of oppression in the Czech Republic, and so opposing the church is in many ways part of being a Czech.
And yet much of this
protest was in the form of other expressions of religiosity. This is the home of the 14th century reformer Jan Hus, whose monument dominates the old town square in Prague and who led to the birth of the Moravian Church.