Because the Native American population would basically have been, in historical epidemic terms, a "virgin field". They had no prior exposure to smallpox, mumps, measles or anything of that nature. Also, communities of Native Americans were relatively small and spread about. They were a lot cleaner and more hygienic, generally speaking, than Europeans were. This meant that the areas they lived in were not the perfect breeding grounds for disease that the foul, jam packed, rat and flea infested European cities had been for thousands of years. This meant that fewer diseases prospered in Native America and there had been no Natural Selection going on for Disease Immunity for most of the time the Natives had been here.
So when the European "settlers" arrived, it was a true slaughter that started the moment one of them touched one Native.
Also you have the fact that many Europeans intentionally weakened the Natives by forcing them into slavery in gold mines and on plantations. The Natives were the original slaves long before Africans were ever forced here. The backbreaking work and unrelenting cruelty of their masters (spanish mainly) tore up their bodies, immune systems and spirits as much as anything else did. Whole tribes, such as the original people Columbus met, the arawaks, were subjected to what amounted to slow, halfway intentional, genocide. I don't think there are any Arawaks at all anymore, and if there are, there can't be more than a handful. Same goes for most of the first contact peoples.
Later on British and American troops intentionally spread disease, in one case by sending a "gift" of smallpox infected blankets to a rebeling Indian Tribe.
Even late in the 19th Century, epidemics were still breaking out, often owing to chronic malnourishment on the Reservations.
