Cortez had around 500 men. Even if you get rid of 99% of the local population, which they didn't, they'd have been outnumbered in to an absurd degree.
In the battle of Frankenhausen, Germany, 1525, German peasants went up against armored soldiers and the casualties were 5000 peasants dead vs 6 armored soldiers. The technological advantage before modern firearms for formal armies was enormous, even in Europe, even without the help of imported European diseases.
If that's 500 fighting men, that's actually a sizeable army. Especially with no supply train.
An army is more than the number of men around. Losing 99% of the population (or even much less) is instant collapse.