In a nutshell: they are a way of doling out some bounty to Bush's faithful base, they are not a way to replicate the services of trained professionals and they are going to lead to cases like this one:
As far as the Rev. John Maxfield could tell, everything was fine between his church and Anoka County until that Friday the 13th.
The county social services department was sending disabled seniors and other vulnerable adults needing care during the day to Trinity Lutheran Church in St. Francis. Trinity's members were bringing in hot dishes for lunch.
Then the county brought another client to the conservative Missouri Synod church: a woman who had begun life as a man.
The church refused to let her in. The county refused to send any more clients.
Maxfield, who says the church now loses significant money on the program, is left to wonder what the future holds for faith-based government-supported social services.
"It places the church in a difficult situation," he said. "We want to minister to everyone. But this person's outward behavior contradicts the church's teaching."
This example may be about a state-level program (I'm not sure) but there is no reason to expect that the federal program wouldn't face the same problem: religious people want to treat their clientele based on the teachings of their church, not based on the needs of that clientele, and religious people want to have the right to discriminate in this manner.
But the money they use is from taxes possibly paid by the very types that these faith-based programs would refuse to serve. Now this is plain wrong.