The Spanish were generally said to have had three motives during this time. They were "God, gold, and glory." The first two of these had the most influence on their attitudes towards the natives.
Both of these motives influenced the Spanish to look down on the natives. They were seen more as tools to be used than as real human beings. Even when they were converted to Christianity, it was often forcible rather than through persuasion.
The desire for wealth had more impact overall on Spanish attitudes. It led them to create the encomienda system in which the Indians essentially became serfs of the Spanish. The Spanish were supposed to care for their souls as well, but the desire for wealth (as can be seen in writings such as those of de las Casas) generally seemed to come first.