This is a huge question with many facets and one which covers a lot of time. During that time, there have been many different federal policies with regard to the rights of Native Americans. In general, we can say that policies did not support the rights of the Native Americans for most of this time period. Recently, however, Native Americans have come to enjoy more rights.
In the 19th century and early 20th century, Indian rights were almost nonexistent. Wars were fought against them and they were put on reservations. Their children were sent to boarding schools which tried to get rid of their native culture. Native Americans were not citizens of the US until 1924 and did not fully enjoy the right to vote until the 1940s.
Recently, more respect has been given to the rights of Native Americans. This can be seen most clearly with respect to things like fishing rights and the right to conduct businesses like casinos.