Taxing churches would then be a way for government to suppress and eliminate religion/religious organizations they do not like. Start taxing today with a "reasonable" tax, and tomorrow you can raise tax obligations until operation is unsustainable. A la "subsidize things you want more of, tax things you want less of".
Despite what non-religious and/or anti-religious people may want, this is untenable and almost certainly unconstitutional.
As an aside - the federal government has plenty of money. We don't need to go looking in the seat cushions for pocket change. Instead of "Reining in America's $3.3T Tax-Exempt Economy", we should be "Reining in America's Overindulgent Lifestyle and Runaway Spending Spree".