From The Penguin History Of Latin America, by Edwin Williamson (Penguin, 2003), Kindle pp. 101-102:
In summary, the Christianization of the American Indians was highly uneven. Difficult though it is to gauge the depth and quality of religious experience, the overall result of the heroic endeavours of these quite small bands of Spanish missionaries was a syncretism of Catholicism and Indian beliefs for large numbers of natives: beneath the externals of Catholic practice there often persisted an attachment to pagan rites and beliefs. Nevertheless, the balance between paganism and Christianity varied widely from one region to the next, and even between individuals no doubt. Sometimes pagan survivals might endure as little more than popular superstitions or dabblings in magic and sorcery, much as they did in remote parts of rural Spain or Ireland. In the Andes, on the other hand, the residue of pagan beliefs was far more evident and, in many secluded regions of America, pagan cultures survived virtually intact.
Still, there is no doubt that Catholic rites and devotions were observed in the vast majority of Indian settlements throughout the principal areas of Spanish rule. What is more, the sacramental character of Catholic belief, the cult of the Virgin and of the saints, the ritual of the Catholic liturgy, the opulence and splendour of religious architecture, art and music, undoubtedly appealed to the Indians and served to transmute pagan religious feeling into new Christian forms. A remarkable example of this is the cult of the Virgin of Guadalupe among the Indians of Mexico. The church that commemorates the appearance of the Virgin to the Indian peasant Juan Diego in 1531 stands on the site of an Aztec shrine to the goddess Tonantzin, Mother of the Earth. Similarly, the practice of penitential self-flagellation among some Andean peoples may derive from kindred acts of expiation in their ancient religions.
The missionaries themselves evidently had reservations about the effectiveness of their campaign of evangelization. In Mexico, there were early attempts to train a native clergy, but these were abandoned by the 1560s, and, thereafter, Indians were deemed unfit for the priesthood. Despite some efforts by the authorities in Rome in the early seventeenth century to encourage the recruitment of Indians, the clergy of the Indies remained white until well into the eighteenth century. Mestizos were also excluded from holy orders, ostensibly because of their illegitimacy – though there was clearly an element of racial prejudice, for the situation did not improve even after a papal dispensation for illegitimate mestizos was granted in 1576.
The result was that the Church remained a Hispanic and colonial institution and, for all their dedication to the Indians and their defence of native rights against the settlers, the missionary orders never relinquished a tutelary and paternalistic attitude towards the native peoples.