There's sort of the obvious notions that many of "faith-based" organizations may discriminate in their application of charity or in their hiring of people for these problems. But even religious organizations that handle these functions correctly, as well as any other type organization (business, another non-profit) with a non-profit branch, can benefit from a little "free advertising" with the help of tax-payer dollars. Ideally, any sort of charity dollars probably should be limited to stand-alone charities, all of which must not discriminate against any in a broad range of factors in terms of hiring, purpose, or service.
I've generally felt the United States government has a conservative wing and a really conservative wing.