I imagine their issue is that they consider themselves 'culturally Christian' and want to still attend without having to lie to get in. If it's purposely to destroy the institution, that's a different kettle of fish. In any case, for churches actually subsidized by state taxes, the atheists have a case. Part of the price countries with 'official' religions pay. The reasoning doesn't apply to churches in the USA. I agree that tax-exemption does not equal subsidy, and it would be a violation of the free exercise clause.