I’m surprised to find such rhetoric on this site. There is an image now popularized by certain political activists and ideologically-driven cartoons, which depict the colonization of the Americas as a mockery of the D-Day landing, with peaceful Natives standing on the shore and smiling, while gun-toting Europeans jump out of the ships and start shooting at them. That image is even more false than the racist depictions in the late 19th century glorifying the westward expansion of the USA while vilifying the natives.
The truth is much more complicated than that.
If you look at the big picture, there was no such conquest in America like the Mongol invasion. There wasn’t even a concentrated “every newcomer versus every native” warfare. The diverse European nations fought among themselves a lot, the Natives also fought among themselves a lot, both before and after the arrival of the Europeans. Europeans allied themselves with the Natives at least as often as they fought against them. Even the history of the unquestionably ruthless conquistadors like Cortez didn’t feature an army of Europeans set out to exterminate a specific ethnicity. He only had a few hundred Europeans with him, and had tens of thousands of Native allies. If you look at the whole history from the beginning, there was no concentrated military invasion with the intent to conquer a continent. Everything happened during a relatively long period of time. The settlements coexisted peacefully with the natives in multiple occasions, traded with each other, and when conflict developed between them it was no more different than any conflict at any other place on the planet. Conflict develops sooner or later, in the new world just as in the old world. Although there certainly were acts of injustice, the bigger picture is that there was no central “us vs them”, not in any stronger form than how the European powers fought wars among themselves. The Natives had the disadvantage of the diseases as other commenters have already stated, but also of the smaller numbers, of the less advanced societal structures (the civilizations of the Old World needed a lot of time between living in tribes and developing forms of governments sufficient to lead nations of millions) and of inferior technology. The term out-competed is much more fitting than exterminated, which is a very biased and politically loaded word.
You cannot compare the colonization of the Americas to the scenario when a starfleet arrives to the planet and proceeds with a controlled extermination of the population.
True, the scenario is not implausible for a non-hostile alien civilization to arrive who are more efficient than us, and in the long term they will out-compete and out-breed us.
Such non-hostile assimilation is not unheard of in real life. It is happening now (or at least claimed by many to be happening) in Europe, both in the form of the migrant crisis and also in the form of smaller countries fearing that their cultural identities and values are being eroded by the larger, richer countries of the union.