The general opinion so far seems to be that "faith-based" organizations in the United States don't want the federal funds that George W. Bush is offering them. The reason, of course, is separation of church and state -- for these organizations to use the funds, they fear that they would have to change exclusively to charity and humanitarian work and eliminate evangelism or outreach.
In fact, a federal law to promote just this sort of thing was passed back in 1996, and staggeringly few states or organizations have taken the government up on it. The new Office Bush has created is simply part of his effort to expand that law further. It was called "charitable choice" back then and was issued as part of an overhaul of the national welfare program, allowing groups to receive tax dollars without changing their religious charters, provided the government's money wasn't used to promote their religion. Five years later, thirty-one states have still not used these federal funds, fourteen report a handful of government contracts, and only five have fully embraced it.
The organizations are reluctant to accept federal funds because of that "no religious use" clause, and rightfully so. Even when these organizations aren't directly promoting their faith through their humanitarian activities, the indirect connection is there. A soup kitchen may want to distribute copies of the Bible or share in one-to-one outreach; a larger organization like Catholic Charities may make efforts to connect those they help with nearby churches for additional physical and spiritual support. Using federal funds would mean they'd have to curtail these outreach efforts or else separate them very, very carefully in their bank accounts.
On the whole, most organizations believe it's not worth the trouble. They've been getting along fine without government sponsorship so far, on the Biblical belief that "God will provide." Having their evangelical hands tied just to take advantage of more mammon goes against everything a truly faith-based organization believes in.