That quotation does exist
I've been curiously watching the flutterings about this in the news for the past week or so - the Seattle Atheists are running a bus ad campaign featuring quotations by Jefferson and some other people. (You can see images of all three ads here.) Before anybody asks, that is in fact a genuine Jefferson quote - it's from a letter to Peter Carr, August 10, 1787. It's in the Encyclopedia! I might note, however, that there is a slight error in the bus ad - Jefferson said, "question with boldness even the existence of a god," while the bus ad says, "question with boldness even the existence of God." Not that anybody will probably care except me. I won't even mention the extra preposition they've inserted. That would be nitpicking.