Joseph,
That isn’t exactly right. Federal law requires that municipalities show “a compelling interest” before enforcing zoning laws against religious institutions (other than wanting them to comply with zoning laws), and that the zoning law is the least restrictive way of achieving that interest. For example, let’s say a Town has a law stating that houses of worship must be on lots larger than 2 acres and you want to open a shul on a lot that is an acre and a half. You apply for a variance and are denied. You can then bring the Town to Court and force them to explain why they have this law.
If they answer, that they don’t want to have parking issues on the street so they want to make sure that the house of worship has sufficient parking spaces, the Court will say that the Town could have achieved that goal by simply making parking on the street illegal in front of the shul. The zoning law will then be invalidated and the Town will have to pay your attorney fees.