Religious persecution, or overbearing regulations?

Here is what the Supreme Court has said:

"Our decisions reveal that the latter reading is the correct one. We have never held that an individual's religious beliefs excuse him from compliance with an otherwise valid law prohibiting conduct that the State is free to regulate. On the contrary, the record of more than a century of our free exercise jurisprudence contradicts that proposition."

I'm assuming that is based on the idea that unless the act is done with the specific intent to restrict a religious practice. Of course, I've never been a big fan of rights being protected by "reasonable procedures" as opposed to actually being given their full effect.

I'm also wondering how any City ordinance regarding free assembly and permits can be allowed to apply to private property, especially a private home? I'm not sure that would be a "reasonable restriction" under any but the most severe circumstances. i.e. the Branch Davidians.