That depends on the religion. For a bit more context (read the full history in [1]): As part of the 1800s separation between state and church, the major ones (Catholic and Evangelic-Lutheran) got the right to a percentage of employed people's wages as a sort of "membership fee". This gets deducted by the employer out of your paycheck and collected by the tax office, then distributed to the church you're a member of. Over the years, the right to collect these taxes expanded by quite a number, although currently only the Roman Catholic, Old Catholic, Evangelic-Lutheran, Free Protestant and Jewish synagogues use that right.
In real life, no one but HR at onboarding cares which religion you specify.
Also note, this is not exclusive to Germany. Italy, Sweden, Austria, Finland, Denmark and Switzerland all have a similar system.
[1] https://de.wikipedia.org/wiki/Kirchensteuer_(Deutschland)