In Article I, the United States Constitution accomplishes the goal of excluding states and individuals from Indian affairs by stating that only Congress has the power “To regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes . . . .” The United States Supreme Court has interpreted this language to mean that the Congress was granted the exclusive right and power to regulate trade and affairs with the Indian tribes. So, individual people could not and to this very day, can not make dealings with Native tribes. While the Constitution originally specified that Blacks were 3/5s of a person to be counted (3/5's compromise), Natives were left out of citizenship count unless they paid taxes. Even after the ratification of the 14th amendment (1868), Natives inside the US territory were still not considered a count towards citizenship, and regarded as citizens of their sovereign tribe. This trend would not be broken until roughly 1924, but there was still hesitation among state government to count non-taxpaying Natives as citizens afterwards. Also, From 1492 forward, European countries and the United States justified their dealings with the natives and American Indian tribes in North and South America under the “doctrine of discovery.” Under this principle, the European country that first discovered a new area where Christian Europeans had not yet arrived could claim the territory for their own country. The US government would continue this policy after their independence, and in 1823, a court case, Johnson vs. McIntosh, reaffirmed this. This excerpt is taken from Native America, Discovered, and Conquered: Thomas Jefferson, Lewis and Clark, and Manifest Destiny:

In exercising its control over the American continent, the United States also enforced the doctrine of discovery. Thus, as the United States Supreme Court stated in 1823, in the case of Johnson v. McIntosh, 21 U.S. (8 Wheat) 543 (1823), the United States acquired the sole right to buy lands from Indian tribal governments under the doctrine of discovery. Thus, sales of land that Indians had made to persons other than to the United States government were invalid. Tribes continued to have the right to use and occupy their lands but their governmental sovereign powers were restricted in that they could only sell their lands to the United States. Johnson, 21 U.S. at 573-74. The United States gained this power under the doctrine of discovery from England and from other European countries as the U.S. bought or acquired the “discovery” authority of these European countries over various parts of the American continent.

So, by putting a legal spin on things, the US government could take whatever they wanted from the Natives for any reason they came up with, and begin allowing or pressuring settlers into the land, without plausible cause.