Since the original claim is that Obama contradicted Jefferson (and presumably by implication that Obama didn't understand the founding principles of U.S. government), I think the quote attributed to Jefferson is fair game for an answer.
According to the Thomas Jefferson Foundation, nothing resembling it appears in the papers and biographies of Jefferson.
The earliest appearance of the phrase that they found is The Barnhill-Tichenor debate on Socialism (1914), where it appears in one of (John Basil) Barnhill's sections, in a list of bons mots. It isn't clear whether Barnhill originated it, but there is no mention of Jefferson.
The earliest attribution to Jefferson that they found was from 1994.
For the Obama quote, see Andrew Grimm's answer.