Here is the main cause why the conquistadores won:

80-90% of the natives died from European diseases before they had a chance to oppose the invaders. This was purely accidental! 300 years before germ theory, no one knew how and why this happened, but in the end conquering nations that were mostly dead already isn't that hard.

Of course, the conquistadores were incredibly cruel by modern standards, as were the natives. But that's not why they won.