Many Native Americans thought "freedom" meant the ability to keep their ancestral lands, to practice their religious beliefs, and continue their traditions. These freedoms, however, did not integrate well with American society/culture.
One of the reasons why white Americans constantly conflicted with Native Americans was their lack of desire to become assimilated into American culture. Native Americans, for the most part, did not want to be forced to speak English and dress like other white Americans. Many times, the effort to not assimilate backfired, as the government created Indian Boarding Schools in which Native Americans were forced to abandon their language and traditions.
Along with this, many white Americans did not want Native Americans to have citizenship because they felt that white Americans were superior to this group.