Religion takes many forms in Tabletop RPGs, but the most common form in the fantasy line that has passed down through D&D and Pathfinder is the pantheon of gods, each god with its own set of particular concerns. More famous and powerful churches might oversee large concepts, like Justice, whereas some smaller churches may be practically obscure – the Forgotten Realms had a deity who went from being the god of death, murder, and tyranny to the god of fatalism.
This degree of diversity requires us to take a second look at how PCs and society at large would interact with religion. Much of the text written on where religious and secular societies meet seems to act as though the churches would occupy much of the same role in the game world as the Catholic Church did in our own medieval period. This is problematic on several levels – churches with specific portfolios of concerns will have their influence constrained, unless they can show at least a tangential relation to those concerns. Additionally, the prevalence of churches with competing philosophies makes the stamping out of heresy a less likely proposition. Of course, a great many inquisitions and heretic-burnings were, in fact, driven by the secular government, which used money or intimidation to get a holy imprimatur on their work. That’s definitely a story.
So, what ought we to bear in mind when speaking about the church. Four general constraints come to mind.
1) Gods are (probably) real. There is a discussion thread on the Paizo forums about the difference between atheist and dystheist practices, and that’s helpful here, because atheists have a somewhat harder uphill argumentative climb to make in a world where worshippers of gods are granted magical powers, to say nothing of places like Faerun, where the gods occasionally drop in for a visit. You can make the argument (as the Golarion nation of Rahadoum does) that the Gods are unworthy of our worship, but arguing against their existence is probably unsound.
2) Gods have specific concerns, humans do not. In a polytheistic society, the average layperson will probably pray to any of half a dozen gods daily, depending on their concerns. Your profession may drive you towards one particular church at least once a week, but even the most devout laity is unlikely to pray to the god of love and beauty for a good harvest.
3) Churches are unlikely to dominate secular life without secular support. This one is more true in our own world than many church critics might want to admit (Philip II’s debts to the Templars had a lot more to do with their being declared heretics than anything the Pope thought), but it should be obvious in a fantasy game world. Since so many faiths have an opposing church, most churches would probably focus more on promoting their own ideals than on trying to purge the unbelievers, since the unbelievers have gods of their own to back them up. Speaking of which…
4) Antagonizing the faithful has consequences. I’d post a link here to a “Here’s how we tormented the paladin in our party” thread, but I can hardly decide which one to choose. Aside from the out-of-game concerns over making another player’s game experience miserable, which violates Wheaton’s Law, there’s a perfectly sound reason not to do so in-game – see constraint #1. Pathfinder’s really excellent series of articles on the gods almost always includes signs and omens of the god’s pleasure or displeasure. PCs who antagonize the faithful should start seeing signs that their spiritual patron pays attention to these sorts of things and doesn’t approve. Yes, that includes when they’re fighting evil clerics. Reminding PCs that these are servants of higher powers, and not simply different flavors of spellcaster, can help make the institutions that are a part of the world feel more real and more consequential.
It’s worth a GM’s time to consider the relationship of various faiths to the setting of their own games, as that influence will help shape the society the PCs interact with. Whether there’s a state religion, or a generally ecumenical acceptance of some or all faiths, religion is a part of the fabric of these societies, and the person who doesn’t pray to anyone is usually something of an odd bird. Adding attitudes and consequence to your game world will make your players’ experience a little bit more High-Definition.