I don’t know about that. We have to remember that even many (not all, but many) of the most progressive thinkers of that time considered blacks — free or enslaved — to be racially inferior to whites.
Now, while Jefferson was a progressive thinker in many ways, the very fact that he was a lifelong slave-owner who never made an effort to emancipate his slaves despite his own deep misgivings about the institution prevents him from being considered progressive when it came to slavery. If we look back now at the simple idea of one human owning another and treating them as mere property, then it’s hard not to say, “Those guys were assholes.” Yet, we also must look at the context of the times.
I don’t think that Jefferson was an asshole. I think he was a brilliant man who was tortured by the obvious hypocrisy of demanding liberty while personally enslaving dozens of human beings. But the fact that he was tortured by the idea or confused doesn’t make him less of a hypocrite. In fact, it makes him more of one.
Was he racist? He was certainly more racist than we are today, but probably less racist than many of his contemporaries. From what we know, he was good to his slaves. Indeed, many historians believe he had a loving relationship with one (Sally Hemings, of course). But they were still slaves — human beings that he bought and sold like livestock.
You notice that there is no resolution to this paradox — no answer to your question. That’s Jefferson. A paradox that I don’t think we’ll ever be able to figure out.