The Native Americans had no concept of a nation. They were comprised of various tribes that moved throughout the land. There was no centralization, no semblance of a unified government. They lived off the land, had their own cultures, system of belief, and simply......lived life.
A lot of people actually do not grasp about what truly and why it happened when the Europeans came. Some believe the Europeans came on the sole intent to conquer. Some believe it was to instill Christian beliefs onto the natives. Others, and this is a widely held belief, that the Europeans came to simply expand and compound their sphere of influence as the various European nations were very competitive with one another, especially on the colonial front.
The N.A's were not beaten with guns and weaponry. They were not beaten with sheer numbers. They were beaten with goods. They used bow and arrows and other rudimentary(but effective for them) tools and instruments. The Europeans introduced guns, sophisticated traps, exotic food items, and other goods that the N.A's boggled at, and were all too happy to trade land for. As in the past, they could always move elsewhere, as they've always done. The White Man will not encroach upon us for he sees us as his friend, a neighbor.
So, how could in such a short amount of time that a people who for generations had effectively and efficiently lived off the fruits of the land, be reduced to being killed by starvation, disease, and famine? In addition, many were killed in armed conflicts over the new settler's broken promises to provide food, shelter and clothing to a defeated, once-proud people living on a reserved piece of land. It continues to this very day, as our government gives very handsome payouts to Native Americans but yet...N.A.'s suffer the highest rates of alcoholism, depression, and suicide anywhere in the country.
The answer: the introduction of an advanced culture to a far less advanced and educated one. This is a deadly mix and often has disastrous consequences upon the "lesser culture." This is not to say that one set of people are inherently better than another group(where calls of racism begin to come in). In this time period, I mean advanced by shipbuilding, technological advances, science, and philosophy.
Sorry for making this long, but let's look at modern day examples: The West(and more recently China and Japan) is pretty much the sole producer of cutting edge technologies and command complete military dominance. With globalization(methodology of travel, internet, commerce) as a norm nowadays, you are putting high-grade technologies and weaponry into the hands of people who otherwise have not advanced far enough on their own to produce and invent them themselves. This is why we now fear radical Islamic fundamentalists because they now have the capabilities, thanks to Western technologies, to blow up parts of cities and kill thousands at once.......if left completely isolated or shut out from the west, they'd still be fighting with swords and rudimentary muskets and rifles. Western technology has only compounded and exponentially increased the destructive natures of the radical Islamists, and much of the peoples of Sub-Saharan Africa. Where a spear or knife was once used, a machine gun can now be used.