Charlotte reflects that

"Mr. Darcy had considerable patronage in the church, and his cousin could have none at all."

Patronage means that the patron had the say over who was appointed to the churches under his patronage (usually those on lands he owned). Patronage in that sense did/does not include appointing Bishops. I think Charlotte was thinking that Darcy might have a more profitable living than Hunsford.

Influence is different to patronage and I have absolutely no idea how much influence a rich, powerful man would have had then in church politics at that higher level.