http://www.amazon.com/dp/0393317552 Guns, Germs, and Steel by Jared M. Diamond does a great job of explaining this in detail, and not just in the North Americas, but examples throughout the world.
It boils down to a few basic ideas
1: Native american's had no real concept of quarantine. If someone was sick, the extended family would take care of them. In turn the extend family would become infected, and infect the rest of the village/tribe as they travelled.
2: Europeans lived in cities with much greater population densities. Their immune systems were much more accustomed to dealing with a large variety of infectious agents. Whereas the native americans live is small homogenous villages. With very little exposure to outside influences, other than other tribes/villages.
I think the most important takeaway was actually that Europe and Asia have huge swaths of land at roughly similar latitudes, so that it was easy for crops and domesticated animals to spread east/west. Those allowed for more intense agriculture, and along with them went diseases.
Here's the wikipedia page, which actually goes into more depth:
Agreed, Diamond's most salient points are 1) the latitudinal axis of Eurasia compared to the longitudinal one of the Americas and 2) the role of domesticated animals as disease vectors. The stuff about pre-Columbians not paying attention to quarantine is quite frankly rubbish (both because Europeans had no modern notions of quarantine either, and because it's impossible to make a blanket statement about how two continents-worth of civilizations conceptualized disease), as is the stuff about lack of urbanization (at least in the context of present-day Mexico and Peru, which indeed did have urbanization on a scale to rival Europe).
A personal pet peeve of mine is that Alfred Crosby wrote about this stuff in the 1970s (The Columbian Exchange) and the 1980s (Ecological Imperialism) but Diamond gets all the credit for it because he successfully repackaged it for more popular audiences, without adding much.
It boils down to a few basic ideas
1: Native american's had no real concept of quarantine. If someone was sick, the extended family would take care of them. In turn the extend family would become infected, and infect the rest of the village/tribe as they travelled.
2: Europeans lived in cities with much greater population densities. Their immune systems were much more accustomed to dealing with a large variety of infectious agents. Whereas the native americans live is small homogenous villages. With very little exposure to outside influences, other than other tribes/villages.