The federal government pursued a policy of Indian Removal because it wanted to keep white settlers (who were, after all, the ones who voted) happy.
The white settlers did not want to be threatened by or even have to compete with Indians as the country began to expand. This was true even if, as in the case of the "Five Civilized Tribes," the Indians were pursuing a sedentary farming lifestyle. Even in those cases where there was no danger of Indian raids and wars, the white settlers wanted the Indians out so they could have the Indians' land. The federal government had racial and political reasons to remove the Indians and no real reason to refrain from doing so.