Some idiot named David Barton wrote a book called "The Jefferson Lies." He was on the Daily Show talking about it and said that people think Thomas Jefferson was an Atheist and Anti-Religion. For one, he is wrong. He missed the whole point. Thomas Jefferson was absolutely NOT an orthodox Christian by any means, tossing out the whole divinity of Jesus and the virgin birth. This does not mean that he was anti-religious nor does it mean he was not religious. The whole point of Thomas Jefferson on religion was that it had no place in making laws and running government. Religion, Jefferson felt, is something between man and his creator. That does not mean that your religion should not guide your ethics and your behavior. That means your religion should not be enforced by your government.
"It does me no harm if my neighbor says there are twenty gods or no god at all. It neither breaks my leg nor picks my pocket." - Thomas Jefferson.
Thomas Jefferson most definitely supported a Secular Government. To say he didn't is just an outright lie. Come to find out, David Barton is well-know to be a right-wing-nut prolific liar.
.... Anyway - the basic point is that Gay Marriage would have been supported by Thomas Jefferson - at least he would have supported it being legal. I don't think he would have engaged in it himself. His (and other Founding Fathers') solidly held belief could be summed up by his own words :
"No man has a natural right to commit aggression on the equal rights of another, and this is all from which the laws ought to restrain him." - Thomas Jefferson
So, since two members of the same sex getting married does no harm to anyone - neither breaking their leg nor picking their pocket - then, as for Thomas Jefferson, its all good... or at least lawful. The only way it could be banned would be enshrining a specific religious bias into our government - something most, if not all, of the founders and citizens who voted to ratify our Constitution - would find a lot more appalling than gay marriage.