The quick answer is despite the popularity of the "death by disease alone" narrative, ~95% infectious disease mortality after contact was not universal, or really even common. The excess mortality Native American nations faced was the result of a toxic combination of factors including, but not limited to, epidemic disease, the indigenous slave trade, instigated warfare, territorial displacement, resource deprivation, and a host of factors that increased excess mortality while simultaneously decreasing fertility and the capacity of the population to rebound.

Please check out the Disease in the Americas section of our FAQ for more information. Also check out this answer for more info on the "death by disease alone" narrative.