Having the church hold the deed to people's eternal soul is quite powerful... also the church has a greater moral authority to rule (God says so is the ultimate trump card ). That's why the state loathes the church if it can't control it.
Discussion
Well, considering the Black Death caused a large disruption of faith, it mostly harmed the foundation of the church. People moved towards more personal spirituality.
I can understand why. If the Church says it is the sole speaker and truth teller for God, but death still sweeps all of Europe, they clearly weren't telling the truth.
the church didn't represent a large swathe of the population who were not counted and did not live in cities due to mainly being pastoralists herding cattle, sheep and goats around the commons. these people were called 'heathens' as a perjorative especially by city dwelling pompous twat "christians".
You see the same thing post WWI and WWII; huge decrease in faith in Europe. In their eyes, god forsaked them. But alot of them were giving their money and praying to the anti-christ (The Pope). So maybe it was better they became atheists...
Then came to worship new gods in the state, giving it the money to create a war machine like no others before in history.