Religious persecution, or overbearing regulations?

But it's also a matter of what defines "religious assembly". We have a small group at our church, about 15+ counting kids, and we get together regularly. Sometimes it's just for dinner or games, but we may sing some songs and we'll definitely pray. Does that fall into the category of "religious assembly" and therefore I need a permit? Many, many, MANY people have Bible study groups in their homes...it's not "church", but more of an additional gathering to study the Word together with a smaller group of friends. If this is defined as a "religious assembly", then they need a permit? Does that mean every time I have a ladies group for a women's Bible Study in my home, I need a permit?

That's where there's way, way too many gray areas to make a blanket application of zoning laws to any religious assembly. If he was having Sunday church services in his home and was publicly advertising the services, then that's one thing. I agree that zoning laws would apply. But having a small group of people in your home to study the Bible is no different than having people over to play Pictionary, IMO.
If you have people over to play pictionary, every week, and they park all down the street half in people's yards, and in unison the entire group says "praise the lord" over and over and over, aggravating the crap out of your neighbors, who may be sleeping, watching a movie, making babies, etc. but can't go about these things because of constant chatter, car doors slamming, people walking down the street, singing and collective loud proclamations, then you will be in the same boat.