Much it has to do with the level of industrialization in the time of nation-forming society, which corresponds to 19th century in Europe. Czech lands were industrial heartland of the Austrian Empire and the modern Czech nation developed in these time with the industrial boom. Slovakia was agricultural society until 1960's, where national development happened in the agrarian society. Czech society like French, Dutch, British, Scandinavia and significant part of Germany (Saxony or Westphalia) went through social, economic, and cultural revolution in the 19th century, which also supported development of the secular, and liberal society derived from modern, industrious population. Countries that developed their national consciousness at the same time, but were not experiencing first and second industrial revolution missed the development of the secular society. This is very typical for Slovakia, Poland, Ireland, Spain, and Greece. The religion became integral part of the modern nation. Economic level has little to do with this notion. Ireland or Spain has higher GDP than Czech Republic or Estonia, but these two countries are the most irreligious and secular in Europe. The same is valid in Germany. Bavaria is the most religious region in Germany with the highest level of church affiliation and church attendance, and it is the second richest republic in the German's republic. But until 1945, it was rather agricultural state, and industrialization happened after WWII, when Germany lost industrial Silesia, and many German speaking immigrants from Eastern Europe settled there. Even Munich, which is similar size like Prague feels provincial, and church attendance in Sunday is matching Polish countryside. Albania is unique state, and it was only socialist country that implemented thorough secularization and atheism as an official doctrine of the state. In Eastern Europe under communism, religion was NEVER outlawed. Catholic church, while broken and controlled, was never put into illegality, so were national orthodox churches and protestants.
Younger generation is increasingly secular even in countries like Poland, and it will eventually matches the same level of church and religion indifference as do other European countries. This is very clearly seen in the power of the traditional catholic parties and organizations that continuously losing membership. This trend is very visible in Germany, Austria, Poland, Hungary, and Slovakia. In recent Polish election, transgender person was elected, so did openly gay man. The traditional church indoctrination has little to appeal masses, and the church is refusing to address issues that plague modern European society (social inequality, environment, and collapsing welfare system). People are not willing to fund church anymore, and in matter of time, church will look for greener pastures in developing world, Asia or USA.