First of all, the total ruthlesness and singlemindedness and lack of good faith of the Conquistadores, something alien to the Aztecs and Incas and something which they did not fully appreciate until it was too late.
Secondly, the Conquistadores were much better armed than the Incas and the Aztecs who had to make do with wooden clubs and the occasional bronze weapons against iron pikes, swords and a little later, guns. The war horses of the Spanish also intimidated them much.
A third reason often mentioned - but this one especially relevant to the Mayas - was the belief that a 'white god' would at one point come across the ocean, which made the Mayas hold back until it was too late.