In his book Bury My Heart at Wounded Knee: An Indian History of the American West, we can actually find author Dee Brown's thesis clearly stated in the introduction. In the introduction, he states that many myths were generated about conquering the American West, and these myths were spoken by folks such as "fur traders, mountain men, steamboat pilots, goldseekers, gamblers," etc. These myths have helped generate the vast number of history books that have been written on the subject. The one voice on the subject that hasn't been heard is that of the American Indian, or as he phrases it, "Only occasionally was the voice of an Indian heard, and then more often than not it was recorded by the pen of a white man." Hence, we can see his main purpose is to express the voice of the American Indian.
But Brown continues from there to speak of all the ways in which the Indians' voices were recorded, though not always accurately, during the conquest of the West. For example, their voices were recorded through interviews for newspapers and through interpreters translating as they spoke in public meetings. He importantly notes, "Most Indian leaders spoke freely and candidly in councils with white officials, and as they became more sophisticated in such matters during the 1870s and 1880s, they demanded the right to choose their own interpreters and recorders." He further states that in writing this book, he used "all of these sources of almost forgotten oral history," and he did so in order to capture the "conquest of the American West as the victims experienced it" and to give readers a "clearer understanding of what the American Indian is, by knowing what he was."
Hence, we can expand our point above to say that his purpose is to capture the American Indian's voice in order to give the reader a better understanding of the Native American by looking at who the Indian was prior to and during the conquest. So, yes, while painting the atrocities of how the Native Americans were treated is a part of his purpose, it's definitely not his main purpose; that's more of a secondary point. His primary point is to express the voice of the Indian in order to show who he is.
One example that illustrates his main message can be seen in his recording of the voice of Maneulito, chief of the Navajos. For years, Maneulito led warriors in a resistance against the US military, which planned to force the Navajo people to relocate from what is now Arizona to Bosque Redondo, New Mexico, a relocation that became known as the Long Walk. Brown records Maneulito as saying he refuses to leave "My God and my mother ... I was born here. I shall remain. I have nothing to lose but my life ... I have never done anything wrong to the Americans or the Mexicans. I have never robbed. If I am killed, innocent blood will be shed." ("Chapter Two: The Long Walk of the Navahos") Through this speech alone, we can hear the devotion, the eloquence, and the heart and mind that Brown is trying to capture.