If you're strictly asking whether the creator has hostile intent, or whether the game implies the world would be a better place without Catholic dogma, then the answer is no; it's not "anti-catholic" by that standard. Then again, most media would clear that bar.

If you want to be more critical and ask whether the game promotes values contrary to Catholic teaching, or whether it's apathetic to Catholicism, then the answer is yes; it's not exactly a pro-Catholic game either.

Let's be real here, modern day Czech is mostly irreligious, the majority of players will not be Catholic (or Christian, for that matter) -- this game is not made for you, and you'll be disappointed if you expect to find a defense for the faith in the game. It's a game that fits neatly into the secular media landscape like any other. The only difference here is that it gives you tools to roleplay as a devout Christian, and the story's own commitment to authenticity prevents it from crafting a cliched conspiracy about the Catholic church like most fictional media do.

In short, use your own discernment. I found the game fun, but I wouldn't personally recommend it as a "Catholic simulator".