No they should not. There is no Constitutional Amendment which prohibits the government from regulating the establishment of Businesses. It seems Churches are tricked into filing into a status that allows the IRS to regulate them. Churches are inheriently exempt from federal taxes under our Constitution and should not need a special filing status.
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.
No, they're not. Churches can be taxed on par with any other entity. The Constitution only prevents the government from taxing a religious organization at a higher rate than non-religious ones.