Because many places were already named and it was easier to keep the names. Just look at all of the places elsewhere in the US that are named for native tribes or native language words.
These states are all named for native tribes or words:
Massachusetts - Algonquin word for 'at the great hill'.
Connecticut - Algonquin word for 'beside the long river.
Delaware - The Delaware tribe.
Ohio - Seneca word for 'great river'.
Indiana - Settlers term for 'land of the Indians'.
Michigan - Ojibwe word for 'large water'.
Illinois - French spelling of the Illini tribal word 'illiniwek', for 'best people'.
Iowa - English proununciation for the Ayuxwa tribe.
Wisconsin - Miami word for 'it lies red', a reference to the red sandstone the now-Wisconsin River flows through at the Wisconsin Dells.
Minnesota - Sioux for 'cloudy water', for the often cloudy skies reflecting on the 'Land of Lakes'.
Nebraska - Oto word for 'flat water' (today, the Platte River).
Alabama - A combination of two Choctaw words for 'vegetation' and 'gatherers'. The people of the land were primarily engaged in agriculture to support themselves.
Mississippi - This one is interesting because it's derived from ore than one tribe. The Ojibwe and Algonquin tribes used the word 'misi-zibi' for 'great river' and the French somehow got Mississippi from it. The Chippewa, a branch of the Ojibwe, also used it. French missionaries moved from down the Mississipi River and took the name with it.
Missouri - another curious case. Marquette first recorded the name Oumessourit, taken from the name the Illini used for the people that lived along what is now the Missouri River. It meant 'land of the canoe people'. These people did not use the name for themselves. They were descended from the Oneota tribe. Marquette apparently never learned the name they called themselves.
Arkansas - another French translation, of 'akakaze' which was the Quapaw (Kaw) word for 'land of downriver people' and Sioux for 'people of the south wind'.
Kansas - After KaNze, a word for 'south wind' used by many tribes who lived around or passed through the region - Kaw, Kansa (Sioux), Omaha, Osage.
Oklahoma - Choctaw word for 'red people'.
The Dakotas - Sioux (also Lakota) word for friends, allies.
Wyoming - Delaware or Algonquin word for 'big prairie'. The name was in use in areas where both tribes had lived, and apparently traveled with the pioneers that settled Wyoming when they moved west.
Utah - Ute (Shoshone) word for 'mountain people and Navajo for 'higher up', the word they used for the Ute people.
Alaska - Aleut word for 'the object toward which the action of the sea is directed' - a convoluted way of saying 'the mainland'.
22 states - nearly half.
Where I live, in the land populated by numerous tribes of the Iroquois nation, counties, cities, towns, villages, rivers and streams all bear the names of those people or the words they had for the land and its features.