I thought your question deserved an answer, so even though it is a little outside of my area of expertise and even though this is such a colossal question that it is hard to know where to start, I thought I would try to explain a little bit the collision between cultures that led to the faiths that we see today. If you don’t mind, I’m going to expand the area a little bit to include South America too, which I feel more comfortable discussing.

I suppose you are correct in finding it surprising that indigenous people converted to Christianity. But the first thing we have to address is that this conversion did not happen overnight. It’s not like the day after the conquistadores moved into a territory all the Native Americans said, “well, we should be gettin’ to church.” The conversion of indigenous people took centuries. Despite being forced to switch religions, Spanish priests frequently complained that indigenous conversions were shallow at best. Even after generations, one priest stated in Mexico that “they have little affection for the church, mass, and holy sacrifice.” This makes sense considering that in many cases, religious concepts like heaven or the trinity simply did not exist. Because of this, priests often had to relate Christian messages to indigenous religious concepts that did exist, which made conversion less of a stark change.

As a result, indigenous people often incorporated their past religious views into new Christian doctrine, which is known as syncretism. For example, in Peru according to Steven J. Stern in Peru’s Indian Peoples and the Challenge of Spanish Conquest, “as in other peasant societies, the authority of Andean gods and chiefs rested in part upon a pragmatic base. Their continual success..sustained their prestige and authority. The Spanish conquest raised doubts about the continuing potency of the Andean gods, while ‘proving’ the risk of offending the Christian deities. Huamanga’s peoples chose to follow a time-honored Andean strategy. Instead of rejecting the powerful foreign deities imposed upon local life, they sought to absorb them into the pantheon of supernatural powers with whom native peoples sought ‘balanced’ relationships” (p. 57). So Andean converts initially recognized that both religions had legitimate deities; Christianity just had the most powerful deities of all as demonstrated by Spanish victories. In this case, indigenous conversion was not an outright rejection of their old ways. In Central America, according to Inga Clendinnen in Ambivalent Conquests: Maya and Spaniard in Yucatan, the acceptance of Spanish rule and faith “meant nothing about acceptance of Spanish claims to exclusive rights over the interpretation and administration of the new faith, as constant Maya claims to that authority make clear” (p. 190). Indigenous people melded their beliefs with Christian beliefs, borrowing some elements and rejecting others, much to the horror of Spanish priests and conquistadores. For instance, in the Jesuit missions of Paraguay, the Guaraní blended bird imagery. The Guaraní believed that their deities often took the form of jungle birds, which translated well with the fact that the Holy Spirit is often shown as taking the form of a dove. Guaraní churches were often decorated not with a dove to represent the Holy Spirit but with traditional jungle birds, thus showing a continuity of Guaraní religious traditions. In Mexico, the Virgin of Guadalupe is often seen as the quintessential example of syncretism as the Virgin appeared as an indigenous woman. So it is not that indigenous traditions died immediately. They persisted and combined with Christianity, in the process making the transition between faiths more gradual.

You are also completely right; there was an incredible amount of resistance. Most obviously, indigenous people resisted initial Spanish incursions fiercely, and even when they were subjugated, there were occasional revolts that sometimes stemmed from religious cults. Many indigenous people continued to worship their old deities for generations, often in secret. Indigenous people ran away from encomiendas, and entire groups of indigenous people moved out of their traditional areas to avoid Spanish incursions all together. Resistance took many forms and prevented the process of conversion from being an instantaneous conquest, further stretching the timeline of conversion over generations and centuries.

The final key component of indigenous conversion that I want to point out is that many indigenous people used the religious relationships with their new Spanish rulers to their advantage. Many Native Americans realized that if they accepted Christianity, or at least gave the illusion of such, they received better treatment than those who didn’t. For one, they might not be enslaved completely but rather only pay a labor tax. It also allowed them to use Spanish judicial systems to file grievances and protest colonial policy decisions. For example, indigenous people in Peru used the Spanish court system to file grievances, protect land rights, and protest mistreatment. According to Barbara Ganson in her book The Guaraní under Spanish Rule in the Río de la Plata, the Guaraní willingly chose to enter the missions, converting to Christianity in the process, because the missions offered far more safety from Portuguese slave raiders and Spanish encomenderos. Once in the missions, they used the Jesuits as a tool to unlock Spanish institutions, frequently writing letters to Spanish leaders to advance their own interests. In Central America, the same is true. Some conversions were harsh, but other priests worked to protect indigenous rights and understand their language and culture.

I don’t want to paint too rosy of a picture. The relationship between Spaniards and indigenous people was still an unequal and oppressive relationship filled with examples of cruelty and atrocities. However, there was a lot more going on than violence. The relationship was a two-way exchange that eventually grew into the religious dynamics we see today. Perhaps by looking at the relationship in this way it will make more sense how conversion could happen gradually over centuries, despite the violence involved.