Dude, all of the laws established by Congress are not specifically enumerated in the Constitution. That does not mean the laws are unconstitutional. You won't find a 65 MPH speed limit listed in the Constitution. That does not mean that a highway with a posted 65 MPH limit is unenforceable.
Under the commerce provisions of the Constitution, Congress has regulatory powers. Along the way, they established businesses would pay taxes. Churches are no different, but in order to give churches and worshippers a break, the conditional non-profit status was implemented. So, either churches play by the rules, or give up their non-profit status. It really is as simple as that.
Dude, the First Amendment does not specifical say Congress shall not regulate speed limits, although it does specifically protect the establishment of religion.