I remember reading a quote somewhere from a British officers diary which said something to the effect that "this rebellion won't be put down until we eradicate every last damn Presbyterian". Which kind of makes sense, given the Presbyterians' substantial contribution to the Parliamentary cause in the English Civil Wars.
The Anglican Church went from being the biggest to almost nonexistent. The first Anglican Bishop in the US (there was none in colonial times) had been a chaplain in American recruited portions of the British Army.
Incidently, Jews petitioned for the clause in the Constitution banning religious tests, citing their contributions in fighting and financing the war. Any test would likely have required the office holder be Christian or Protestant. However, the main reason it was included was that test in colonial times had specifically required the holder be Anglican or Congregationalist depending on the colony. Tests in Europe required the holder to be Catholic, Lutheran, Orthodox, and Muslim, depending on the country.