The reason is on the Wikipedia page for "Little House on the Prairie" in the section "Depiction of minorities". I think it's important to understand that this is period literature and that there might be ideas in the story that may no longer be considered acceptable or may seem odd to us now - history has a tendency to work that way. But as the Wikipedia article points out, "...these portrayals do not necessarily represent the views of the author and there are very positive portrayals of native American and black people."

I read "Little House on the Prairie" to my niece when she was little, and I fully intend to read those books to my daughter when she's old enough to understand them. I think it's important that she have an understanding of what the past was like.