Zoning is a big area where churches often are found to have more freedom. The basic argument is that putting arbitrary restrictions on a church is a violation of the 1st Amd.

There is nuance, such as, if the state can prove to a court that a zoning restriction is necessary. For example, a rule against high occupancy buildings in a flood plain, or the like, may be okay. While a rule against off street parking in a residential neighborhood, or the like, may not be enforced against churches.

Generally, US governments get into trouble if they put restrictions on religious institutions that are not absolutely necessary.