Churches should be taxed anyway, not because of anti-religious sentiments but because they take in too much money to NOT be taxed. Especially when a lot of these churches take on political bents either through sermons or through work they do to further/oppose bills and legislation. Take Prop 8 out in California for example.
Once a church takes a political stance on ANYTHING, it's tax-exempt status should be removed. They should be treated like any other entity and taxed on the money it takes in and the property it owns. That money should go to education, unemployment, veteran's benefits, Social Security, Medicaid/Medicare, roads, and a host of other things. The budget/deficit would start to go down.