I always figured Jefferson and the other Deists of the Enlightenment were probably struggling with being an atheist. Religion, on its face, makes no sense to an organized thinker. And since they were all raised in the traditions of the western Christian Church most of them would have defaulted to understanding religion in that frame. So Jefferson took his Bible and eliminated all the supernatural stuff from Christ's actions. That's cool, it's effectively what I do and I'm a full-on atheist. The teachings are good but the idea of the supernatural is useless to me.
There's a possibility they truly believed there was some ineffible being outside of space and time, but I wonder how many were just desperately trying to AVOID falling into atheism.
(And yes I differentiate atheism from agnosticism since the agnostic feels the question can never be answered while the atheist can simply fail to believe in God. The example I gave to another poster is: "You are not agnostic about invisible elephants in the road as you drive but they COULD be there." The question is one of "I don't REALLY fully know". The atheist can answer it by saying "I simply fail to believe there are any invisible elephants in the road in front of me so I don't need to slow down on an open road.")