While Native Americans are counted for purposes of population in the House of Representatives, the case could be made that as sovereign nations, various Indian tribes should have rights to specific representation in the Senate.
Why was this never the case?
Your premise is flawed, Native Americans do have representation in the Senate.
Any Native American that is a citizen of the United States has two senators that represent them in the Senate, based upon the state that they reside in.
Then there is the rather racist definition of "representation" which requires that someone of the same skin color, religious persuasion, etc. is their representative. Even under this definition, there have been several senators with significantly acknoledged Native American ancestry. Charles Curtis of Kansas 1906-1926, who later served as the Senate Republican Majority Leader (1925-1929). Robert Latham Owen, Jr. of Oklahoma 1907-1925.
Finally, perhaps you were just referring to Native Americans on Indian reservations requesting statehood.
The Senate of the United States shall be composed of two Senators from each state. U.S. Constitution, Article I, section 3, clause 1
There is some historical precedence for that. The Oklahoma Territory is composed of both Indian Territory and Oklahoma Territory when both were requesting statehood individually.
Representatives of the Five Civilized Tribes met in 1902 to work on securing statehood for Indian Territory and held a convention in Eufaula. [...] The convention drafted a constitution, drew up a plan of organization for the government, put together a map showing the counties to be established, and elected delegates to go to the United States Congress to petition for statehood. The convention's proposals were presented in a referendum in Indian Territory, in which they were overwhelmingly endorsed.
The delegation received a cool reception in Washington. Eastern politicians, fearing the admission of two more Western states, put pressure on the U.S. President, Theodore Roosevelt. He ruled that the Indian and Oklahoma Territories would be granted statehood only as a combined state.
So, in Oklahoma since 1907 Native Americans of the Five Civilized Tribes have had two senators representing them in the U.S. Senate.
Should every tribe get a Representative and two Senators? As of the 2010 census, Wyoming was the US state with the smallest population: 563,767. The two largest Indian tribes, the Cherokee and Navajo, have about 300,000 members. Then there are 560 smaller Federally recognized tribes, with populations down to the 8 members of the Augustine Band of Cahuilla Indians.
Now all of these tribes are culturally diverse, and many are hereditary enemies. The Hopi and Zuni probably wouldn't be happy to have a Navajo represent them, the Navajo wouldn't want an Apache or Ute, and none of them would have much in common with a Cherokee or Mohawk. So even assuming you can get around racial discrimination laws, exactly how are you going to arrange fair representation for all the tribes?
PS: Indians have the same possibility of being elected to Congress as anyone else. There have been a number throughout history, and (per Wikipedia) two current members of the House. (And of course, there are many Americans of mixed ancestry, who don't consider themselves "Indians".)
