In brief, because it was not just disease that contributed to the demise of most Native Americans. There was a whole host of of other impacts like disrupted settlement and subsistence systems, wide scale enslavement, changes in resource availability, government policies, conflicts with other tribes and wholesale slaughter. Also, some of the epidemics returned in approximate 10-20 year intervals.

This is a difficult, if not impossible question to answer on continental scale. I am going to direct you to our FAQs, especially this one by u/anthropology_nerd for a description of what transpired in the American southeast. I have a much better grasp on what happened in the western North America. So my comments below pertain to that area.

Epidemics in the Northwest started following sustained contact, so for the most part from the 1770s to the 1850s. Smallpox returns in 1800, 1824, 1836, 1853 and 1863 in Oregon. This pattern of recurring epidemics has been observed in many areas of North America. In addition there were recurring outbreaks of influenza (or what is thought to have been influenza), measles, malaria and a number of other deadly diseases.

While these diseases are active, many areas of the west were actively being colonized by white settlers. The settlers, not surprisingly, wanted the premium land that just so happened to be where the Indians lived. Many natives were massacred because they simply were in the way of white settlement. Others moved away often into areas occupied by traditional enemies. Keep in mind that natives were very strategic in developing collecting, hunting and fishing practices. Highly productive stretches of rivers were owned, shared and rented out. The same applied to acorn gathering sites. Once the natives are pushed out of their resource procurement areas, they become stressed beyond their capability to support themselves. Natives of Northern California stored many huge baskets with acorns as a hedge against years with poor acorn production. Once people were burned out of their houses, they had to find new gathering areas and had no stored goods to sustain them.

Government policies were major factors in the demise of the Natives. Local militias, made up of failed miners, or other unemployed men, hunted down Indians for bounties and wages. Because the labors of the volunteer militias was routinely reimbursed by the State, militia members soon learned that fighting Indians was a profitable enterprise. Militias became very adept at removing natives. The common practice was kill any visible Indians then burn their houses.

State policies like the The Act for the Government and Protection of Indians made it possible to indenture/enslave natives. The early treaties and the following reservation system was tolerable if you happened to be an Indian who traditionally lived in the reservation area. For those that did not already reside on land that became reservations, it was a nightmare. People were moved several hundred miles, families were broken up. Women were enslaved. There are a number of accounts of tribes being placed in reservations with traditional enemies.

In Southern Oregon and Northern California the Indians who never got moved to reservations suffered massive disruption. The pattern that emerges for these non-reservation Indians is sobering. The male natives just disappear. The females are either killed or enslaved. Children old enough to be useful were indentured/enslaved. Many of the women later become wives of single settlers.

A not insignificant factor was that many natives not only actively engaged in conflicts with whites but also continued to skirmish and battle other native tribes. These battles were never very large but they provided for even more stress on people and undoubtedly had a tangible impact.

The bottom line is that disease was just one variable among others, many of which had severe and lasting deleterious effects.

Disease Epidemics among Indians, 1770s-1850s Oregon Encyclopedia

Brendan Lindsay, Murder State: California's Native American Genocide, 1846-1873

Boyd, Robert. "Lower Chinookan Disease and Demography." In Chinookan Peoples of the Lower Columbia, edited by Robert Boyd, Kenneth Ames, and Tony Johnson. Seattle: University of Washington Press, 2013.

K. Ames and Herbert Maschner. Peoples of the Northwest Coast: Their Archaeology and Prehistory