Why did the Europeans treat the Africans differently from the way they treated the Native Americans from 1492-1808?

During the period of European colonialism, imperialism, and slavery, race played a big part in the structuring of new societies and the replacement of old ones. White, Christian Europeans were of the belief that God had created many distinct races of the world, but that some were naturally better than others. White Europeans believed themselves to be at the top of this racial hierarchy, considering themselves the most intelligent, most moral, and purest of the handful of simplified racial categorizations- the others being Black, Red, Brown, and Yellow. There were many attempts to scientifically justify these racial categorizations on the basis of bone structure, terminal height, dental health, intelligence quotient, and physical strength, and this gave way to terms like Caucasoid, Negroid, and Mongoloid in referring to people in different phenotypes. Today we know that these socially-structured categories are not based in any scientific, bodily reality, but nonetheless they have a significant impact on  how a person's life is lived.

In the racial hierarchy used during the age of European expansion, white people were considered the only full human beings with rights and reason. People of Color were considered to be closer to non-human animals, by degrees in correlation with skin color. At the bottom of this racial hierarchy were Black Africans, many of whom were captured and forced into slavery in the New World. This was "justified" by the belief that Black people were more animal than whites and needed to be shepherded by white people. Between Black and white people fell Asians and Indigenous Americans. Indigenous Americans were considered to have more of a "capacity" for civilization because they were lighter-skinned and had a culture of respect which Europeans considered noble. 

Though white Europeans killed, enslaved, and forced the assimilation of millions of Indigenous Americans and Africans, there were slightly different attitudes behind both. In their treatment of Indigenous Americans, Europeans felt they could and had given them a chance to convert and become civilized. In contrast, Europeans felt there was no hope to humanize or civilize Black Africans and so treated them essentially as animals for labor.