Show it in the people under the church's boot. The church puts ridiculous laws into place, have the people accept them blindly without question, and those who do question it openly disappear. Have an NPC get a little too drunk and have him speak out against the church. Then he disappears, and nobody questions it. Have the majority of the population believing in the church doctrine and actively participating in the atrocities committed. The people are the ones doing the witch burning, but it's the church that instigated it. Have the church be very bigoted, they dislike members of certain races to the degree that they will not allow them into certain parts of the cities. This is reflected in the way the people act because that's what they believe. The dwarf shouldn't be allowed into the temple district because that's just the way it is for them. The hypocrisy suggestion is really good as is giving the players an physical entity to hate that represents the church. The Cardinal Richelieu as it were.