Congress can pass certain types of regulation (like on taxation - because taxation is a government concern) . . . as long as it's applied FAIRLY to every form of religious 'entity' (church - etc).
It cannot affect one type of faith (like Jewish) and not another (Catholic or Buddhist) by it's inherent nature - direct or indirect. (the case I vaguely remember was very indirect - having nothing to do with religion at all but did impact how a particular religion conducted itself).
I'll look around and see if I can find it. . . it really clarifies how the first is applied an considered in the eyes of the law.