It was disease what ultimately killed most Indians off. Dropped them right and left.
On that site, they write of some plague that decimated the native population before the Europeans arrived. I've read of how the original Spanish explorers spread diseases (primarily smallpox) among the natives that killed many in some areas. But that's not what that site is referring to, and certainly not much later exposure to European diseases after there were many Europeans in the New World.
Like most of the assertions made on the site, the "plague" is not well explained and certainly not documented.
I’d think the constant fighting and wars between tribes might have contributed.