Correct me if I'm wrong somewhere, but... what's so bad about not taxing money given straight to registered non-profit organizations that don't pay taxes themselves? Isn't it more wrong to tax that money to begin with? Do we "owe" that money to the government?
Now, I'm solidly against handing government money to religious organizations, (including "doubling" programs) but that's another matter (though Bush may try to blur them).
Tax deductions aren't the same as subsidies.