theflink: It isn't. Pretty much all characters are catholic, as they were in those times. There is, however, talk of the reformist named Jan Hus, and a guy is into those ideas of what would later become the ideas behind protestantism.
Other than that, nope. Religion is not a central theme, though it is all around.
If you like church art, this should be a nice one since every church is beautifully decorated with period-artwork. Lovely! :)
Martin Luther, another famous Christian, was a fervent critic of the Catholic church--founded the reformation which birthed Protestantism. Many critics of the Catholic church today are Christians. Catholicism and Christianity are regarded as separate things by many Christians living today.
Personally, as a Christian myself, I do not consider attacks on the Catholic church as necessarily negative, especially for doctrines like "purgatory", for instance, in which the relatives of dead Catholics had to pay local priests to supposedly move them from "purgatory" to heaven (and often those relatives were left rotting in heaps above ground until the purgatory fees were paid, at which time they were buried in the so-called "hallowed" ground the local Catholic church owned.) Etc. Lots of critical grist for Catholicism in history. But the same is true for the so-called Divine Right of Kings in the secular world during those times...;) Brutal times, all around.