The concept of Cowboys & Indians being enemies is a Hollywood myth. The US Army killed more Amerinds than any cowboy ever did, and in most cases, the two groups banded together. By the time that the cowboys emerged (the mid-1860s), the native tribes had already been decimated in the previous three decades. Cowboys, marching the cows to the Eastern railroads, often traded some of the cattle to the starving Indians in exchange for help with navigating the land.

This is a good article on the history of Cowboys and Indians in pop culture