Religious organizations (and some other non-profits) should no longer be eligible for tax-exemption, ending the government (and tax-payer) subsidization of religion. While this policy may have had a place in the America of old, nowadays it's a mess of loopholes and bureaucracy where there should be none.
Sure, charitable giving may drop (something defenders of this status quo argue), but government revenue would increase, allowing for more homes for the homeless and public works projects. This would in turn do away with the NEED for some of these non-profits, such as soup kitchens. "Countries that truly care about poverty don’t rely on churches to run soup kitchens." And, if truly needed, localities could always carve out sensible property-tax exceptions for nonprofits.