I've recently finished DMing a campaign involving a powerful monotheistic church that controlled much of the world that my group was bent on overthrowing. Not sure if this will work for your group, but it did wonders for mine;

- Make the church leaders very visible but untouchable and entirely too smug about it. Nothing frustrates and angers my players more than being unable to directly attack their enemies when they can see them! And a generally holier than thou attitude on the part of the badies doesn't hurt.

- Slowly introduce stupid new laws to towns controlled by the church that make the PC's lives annoying; Outlaw drinking after nightfall. Outlaw the carrying of weapons by anyone not visibly wearing a holy symbol of the church. Make it custom to greet people with "By the grace of the almighty and righteous one god, well met" and replace goodbye with "Hallowed be the one god, and fare thee well". Have NPCs get upset if they don't use the correct phrases. Rub their faces in the fact that society is run by these guys.

- Have agents of the church attack the periphery of the PCs world in nasty but technically legal ways; Arrest any NPCs that have helped them and burn them as witches. Purchase and then convert their favourite pub into a church. Have a PC's elderly mother thrown out of the family home on trumped up debts. That kind of thing.

Hope you can get something useful out of that!