Growing up in the American educational system, we learned a lot about the horrible treatment of native Americans as well as African slaves in colonial America. For the latter, we learn a lot about advocates for slaves, and vocal opponents of the institution of slavery. However, I don't recall learning about any sort of equivalent for Native Americans. Were there any notable individuals or institutions (particularly in the caucasian population) who argued or fought for equality/fair treatment of native populations in colonial times?
You're probably asking about the modern day US which is outside my field -- but in case you're interested I've written about this for colonial Latin America before. There especially priests of the religious orders were active in advocating on Native Americans’ behalf since the early 16th century. One major development was the recognition of indigenous people as worthy of royal protection -- tied especially to the Dominican de las Casas. But also Franciscans and other orders in colonial Mexico highlighted the importance of native societies and histories, while branding native beliefs as "idolatrous".
Some more background:
Here on las Casas (More details in the follow ups)
Hope this helps!