See <i>Guns, Germs, and Steel</i> by Jared Diamond (which some disagree with, but an interesting book nonetheless). He says that the key factor was the large number of animal species in the old world that could be domesticated. So Europeans all had constant contact with animals and their diseases, which led to (1) more diseases, and (2) greater resistance (among those that survived). While in the Americas, with their relative lack of such species, the people had both fewer diseases (so they were less of a threat to the Europeans) and less resistance (so the Europeans were more of a threat to them).