As with any such question, there is no one answer. There were thousands of groups of indigenous folk and thousands of explorers, missionaries, sailors, bureaucrats, and nobles who each had their own opinion of everyone else.

One situation which I can describe is that of early colonial Peru. In this setting, the natives were actually respected more than some Eurasian people. I previously addressed issues of race here with my old account, but I'll summarize it here again. Two things were happening at the end of the 15th century in Spain that would create the entire concept of Spanish-ness.

First, Iberia was becoming the Spain we know today. Castille had just concluded the reconquista by pushing out the final Islamic stronghold in Iberia. The Spanish language was being codified. Jews were officially expelled from Iberia. The Inquisition was created to sweep up what this edict and the reconquista left behind. It sought out Protestants, Jews, and Muslims and coerced them to join the Catholic church, or else not be included in the nascent Spanish identity. Protestants and "lapsed" Catholics were nothing to worry about. They had Christianity in their sangre, "blood." Converted Jews and Muslims, however, were called "new Christians" and were still held suspicious.

Second, Spanish colonists were expanding their political influence into the Americas. Here they encountered new people, new beliefs, and new political systems. Shortly, they began to generally divide the people of the colonies into three groups: Castellanos, *indios, and negros (Spanish, native, and African).

It didn't take too long for the Inquisition to cross the Atlantic. It sought out Protestants and Jews and Catholics who had taken a liking to suspected witchcraft... but never natives. They were essentially exempt from its gaze. Why? Most priests considered the residents of the Andes to be somehow "preconditioned" for Catholicism. Christianity was the mark of civilization, and they had shown so many other signs of being a civilized bunch: their orthagonally planned cities, roadways, taxation, military, and empire management all impressed the Spanish. A converted indio was not, in fact, a "new Christian" like the Jews or Muslims. They were considered a step-above them in preparedness for the Spanish breed of civilizing.

Modern Inquisitions Martha Silverblatt