In Thomas Jefferson's vision of America, Native Americans needed to become "civilized" or be removed from the scene.
On the one hand, Jefferson wanted to civilize the Native Americans. In his second inaugural address, for example, Jefferson sets out his ideas about the fate of the Natives. He says that
...humanity enjoins us to teach them agriculture and the domestic arts; to encourage them to that industry which alone can enable them to maintain their place in existence...
As this shows, Jefferson had a vision in which the Native Americans would be helped to assimilate into white society. This was, to him, the only way that they could continue to exist in a country where they had been overwhelmed by the numbers of white settlers.
Jefferson believed that this was the only choice for the Native Americans. They could live as white people lived (and they should be helped to do so) or they could leave the country. As he said in this letter to William Henry Harrison, who was then governor of the Indiana Territory,
...they will in time either incorporate with us as citizens of the United States or remove beyond the Mississippi...
To Jefferson, Americans needed to be small farmers. Native Americans could change to that way of life or they could leave the country. That was his vision for how Indians fit into the new country.