The ways in which these two groups were treated was very different because of the differences in the relationships between each group and the dominant white majority.
Native Americans were not a part of American society. Even after the wars ended, they did not live among the whites and were not important to white society. The government did try to assimilate Native Americans after the end of the wars, but it did so half-heartedly. The main policy with regard to Native Americans was to keep them completely separate on their reservations.
African Americans were a part of American society. Even after slavery ended, they were needed as a source of labor. They lived among the whites in the South. What the whites did was to keep them physically close but to strictly separate them in psychological terms by emphasizing that they were second-class citizens.