Me and my best friend planned a campaign like this, and discussed at lenggth why people got mad at large churches and governments in the first place. We decided that one of the best ways to turn a party against a large, lawful institution is to have them do the same things that such institutions in real life do: combine ridiculous rules with insane graft.
Have the church tax them at every turn. The party should be constantly paying tolls, having random tax men show up and question them about magic item purchases and spells cast, and most importantly: increase the price on liquor to insane amounts.
All of these will generate irritation, but not hatred. That's why you combine it with graft and hypocrisy.
For example, let's say they have to infiltrate a secret society of the church. They go through the elaborate entry rituals through some insane disguise and bluff checks, not to mention creative bribery on the part of everyone else, and enter it. What do they find?
A brothel. A place where elaborate orgies and abuse of the wildest drugs imaginable take place nightly. Where the clients are constantly subject to abuse and hastily covered up deaths: they should probably see a girl covered with bruises and cuts being dragged out. When they meet the church officials, have them BRAG about it. How their superiors turn a blind eye to them, how they spit in the face of the god they worship and get away with it, and how they finance this elaborate den of vice through taxes such as the new liquor tax.
If that doesen't get the PCs blood boiling, I don't know what will.