The answer to this is that the vast majority of deaths among Native Americans in the early years came from disease. In fact, many of these deaths occurred in Native American populations that had themselves not yet contacted Europeans. They got the diseases from those Native populations that had contacted Europeans.
The reason for this was that Native American populations had not immunity to European diseases. They had been separated from the European populations for too long and so had not developed immunity to the same diseases. When the Europeans arrived, the Native Americans were exposed for the first time to diseases like smallpox and measles and died in tremendously large numbers.