For the Aztecs at least, yes and no. They did originally believe them to be the entourage of the returning god Quetzalcoatl, a pale god who would return from across the sea to save them from the Black Sun (I believe, it's been a while since I heard the specifics of the legend), but once they began to interact with other city-states that paid tribute to the Aztecs, and they armed up with the Tlaxcalans, the mortal foes of both Quetzalcoatl and the Aztec people, they realized they were not dealing with their god, but foreign invaders with godlike powers (An important distinction). They also believed their horses to be "giant stags with no antlers," and they also remarked upon the huge size of the dogs they brought. They marveled at their metal armor and large weapons, and believed their cannons could split mountains in half with a single shot (A claim the Spanish were more than happy to perpetuate, and would often shoot cannons to scare the locals if they felt like it). There was talk of them still being gods of some kind (if not their god) until Montezuma and Cortez met formally in Tenochtitlan, and they refused all sacrificial offerings that the Aztecs made to them with revulsion (Including dipping and eating bread into a bowl of fresh human blood, and being flecked with the blood of a sacrificial virgin).

So, yes, they did at first think so, until the Spanish did un-godlike things and they met them in person.