I've been reading Meacham's book on Jefferson and have a few insights you might find helpful. Jefferson was fascinated with the west and he was fascinated with Indian culture. "Jefferson often sought artifacts and information to satisfy a genuine curiosity about America's original inhabitants. He believe Indians a noble race."

But all of this was tempered with the views that Jefferson held, and the views that many men like him held at the time, that the lands in which the Indians inhabited would one day be controlled by the stronger white race and that, "the Indians themselves should be inculcated in the ways of the whites."

And we see this play out when Jefferson was President with the Louisiana Purchase and the subsequent opening up of the west in the following years. So it appears that Jefferson was fascinated by the culture and the people, but that he ultimately believed them to be inferior in comparison to the Caucasian race. And this is evidenced by via views that the whites would one day control their land, and that Indians would adopt the traits of white culture.