90% of the stops are Christan churches
Pokemon religion confirmed?
And the other 10% is university of Waterloo, I can't go 10 feet without getting balls or pokemon
~ @Marshy_88
There are several plausible explanations for that.
First, there is the idea that churches are fairly common, and are usually fine with people hanging around. Given, there are some that aren't, but those are just the oldies throwing a fit about technology. You won't find basically any Muslims playing it because their religious authorities have reinstated a fatwa on Pokemon. Why that is, is none of my business.
Secondly, churches are mostly used only on Sunday, thus Go trainers will not be disturbing anyone. This is the problem with finding Pokemon anywhere in the current version; it does not register altitude, meaning the same Ekans on the ground floor is on the roof of a skyscraper.
Thirdly, this could be Pokemon's way of trying to reconcile with churches that often disliked it. I doubt it is this, but it's possible.
Fourth, it could just be random chance. Churches are common, and public. There's something seriously wrong if they tell you to leave a church's property.