There are many reasons that Jared Diamond presents to explain why Europeans were able to defeat Native Americans militarily. You can find these reasons presented throughout Chapter 3, in which Diamond discusses the factors that allowed the Spanish to defeat the Inca Empire. Another good place to see the factors that Diamond thinks are important is in Chapter 4, Figure 4.1. There, Diamond lays out his general theory as to what causes the broadest outlines of history, which essentially reflect the fact that people who had been farming for a long time, like the Europeans, defeated those who had not, like the Native Americans.
The basic reason why the Europeans defeated the Americans is that they had “guns, germs, and steel.” In other words, the Europeans had better technology, which gave them much more military power. They also inadvertently brought germs, which decimated the native population, making the job of conquering them much easier. These factors, in addition to other related factors like more elaborate political organization and the ability to write, made the Europeans able to conquer the Americans.
However, Diamond is not content to look at just these things, as they are what he calls “proximate factors.” He wants to explain why the Europeans had guns, germs, and steel while the Americans did not. He says that this was because Europeans started to farm long before Americans did. The fact that they farmed first came about because of factors having to do with geographical luck that are laid out in Figure 4.1.
In short, then, the answer to this is that Europeans conquered the Americans because of guns, germs, and steel, and they had these things because their geographic luck allowed them to develop farming before the Americans did.