Overall exposure to disease is an important factor, too. There were many, many domestic animals in Eurasia by 1500, while there very few domestic animals in North and South America. A lot of the disesases common to Europeans (and Asians) came from domestic animals. The people of the Americas did not have resistances to these diseases. There were other important factos, too. A great many of the Spanish conquistadores
had fought with Cordoba in northern Italy before going to the New World. They had been exposed to malaria. Those who were debilitated by the disease generally did not go out to the "new world." Those who were resistant did, and they brought the disease with them.
It was not an entirely one way street, either. Yaws, caused by a spirochete, was common in the Americas. On the other hand, syphilis, which was relatively new to Europeans, is also caused by a spirochete, and Europeans had not developed a resistance. The people of the Americas had had literally centuries to develop a resistance to yaws, and were therefore, largely immune to syphillis (the spirochetes which cause yaws and syphillis are two different species, but come from the same genus--Treponema
The lack of domestic animals amond the aboriginal Americans meant that they were far more vulnerable to a disease such as influenza, which is an avian disease, to which Europeans and Asians have been exposed for thousands of years. Other disease of domestic livestock also devastated the Americans, while having much less effect on Europeans.