The population was already declining when Europeans got here. But it dropped precipitously thereafter, starting almost immediately due to disease. By the 1600s, tribes in the east were nearly wiped out. Since the majority of "explorers" came to America after this time, the accounts of the native cultures reflect an already-defeated society.

For years, it was thought inconceivable that the native cultures encountered in the 1600s could have built such elaborate structures. The common understanding was full of racist overtones - these cultures were too "primitive" to have built cities. Reality is that if Europeans met Native Americans in say 1100, the situation would be reversed - the Americas were thriving with trade and cities while Europeans were largely subsistence-farming peasants caught in the dark ages.

If you're interested in this topic, definitely check out "Origin: A genetic history of the Americas" by Jennifer Raff.