The indigenes and Europeans had different concepts about forests. In the forests, the indigenes imagined many invisible things.
But the Europeans simply wanted to clear the forests and convert them into cornfields.
Jefferson wanted a country with Europeans and small fields. The indigenes cultivated the land for their own use. They did not do it for selling or profit. Therefore acquiring land in their view was a serious mistake. This is what made Jefferson think that they were uncivilized.