Could well be that the "faith-based" program increased government funding for religious charities but it has been going on for a long time. 

Internationally, it is a ritual of the first day of a President who is of a different party from his predecessor to revoke or reinstate the "Mexico City Policy," established by Reagan, which prohibits government support of NGOs that offer counseling related to abortion.

Domestically, I know that Catholic Charities and some of its affiliates receive a large portion of their funding from the government.  Early screams by the bishops about "religious liberty" involved refusal of the government to renew contracts with Catholic agencies that refused to arrange adoptions by gay couples.

I have unwittingly waded into a discussion about something of which my knowledge is neither broad nor deep.  Although that does not make me unusual among NCR commenters, I think I better stop now.