He did have his flaws.
Like any rich planter from that era, he was a product of his time. I'm sure all slave owners had their favorite nigress. Masters imposing themselves on their slaves is as old as slavery itself.
That aside, I like Jefferson for his political views and pragmatism. He believed in a small limited government, but wasn't afraid to step up and take charge when he had to. The Louisiana Purchase was one such example. He didn't believe he had the constitutional authority to do it, but thought it was too good of an opportunity to pass up.
His knowledge and enthusiasm for a wide array of scientific fields (botany, astronomy, architecture, etc) was also very impressive. You can't ever go wrong with a Renaissance man.