The simple answer is that they wanted to convert the indigenous population to Catholic Christianity. The natives of Central and South America were looked upon by the Spanish as heathens, people who did not belong to a recognized religious creed. As such, the Catholic missionaries who accompanied the Spanish conquerors saw the colonial venture as a golden opportunity to bring potentially thousands of new converts to what they regarded as the only true faith.
The Catholic missionaries sought to impose their religion on the native population, but they did so without much success. Many of the indigenous people simply incorporated certain elements of Catholicism with their own traditional beliefs, thereby blurring the distinction between the two. Though the Catholic Church was an active partner in the colonial enterprise, the Catholic Church often spoke out against the brutality and exploitation of Spanish colonial rule and urged the authorities to treat the natives more humanely. Nonetheless, the Catholic Church benefited considerably from the harshness of Spanish rule, as it provided them with a captive audience for their missionary endeavors.