I read the article, and personally think the author is grasping at straws. The Indian wars were not wars of ideology, but rather conquest and while not genocide, it was definitely was racial/cultural. We're coming, join us or get on your reservation.

It was largely an internal war; though other nations used the Indians as surrogates throughout the years.

The war we're fighting now is global (with a homeland defense requirement), it is a war of ideology (political religion) that ultimately will decide what laws and economic models those being fought over will live under. It is a war that is waged on the internet, in the media, mosques around the world, and it is not restricted to tribes (Anyone can become a Muslim from Indonesian, Thailand, N. Africa, Ohio, Canada, etc. regardless of race, not everyone can become an Indian), cover actions, and overtly on the battlefied. It is very much like the cold war, except the nation state (with the possible exception of Iran) isn't the main the threat. Our objective isn't total defeat (we can't do it), but rather to win over large segments of the Muslim population to a non-radical view. During the Cold War our objective was win over large segments of the global population from communism to other forms of government and economic models (we didn't start pushing democracy that hard until after the collapse of the USSR, we didn't have that luxury until then).

There may be several loose parallels to the Indian wars, but it is a stretch, and not near as close a parallel as the Cold War in my opinion.