Through this remark, the author is juxtaposing various ways for the reader to understand "difference," which is an important topic in the novel. Everyone is "different" in this story, from Scout who will not act like the lady her aunt wants her to be, to Atticus who does not hunt or play football as his son would prefer. Bo is different because he is a recluse. Tom is different because he is black, and the Ewells are different because they are poor, white trash, people without roots and therefore without morals. When Atticus tells Scout the lowest sort of man is one who takes advantage of Negroes (such as what Ewell does in regards to Tom), he would seem to deny Scout's conclusion, which would otherwise be a comforting and simple solution to the problem of social discord and hatred.
Scout is taking the stand that all human beings are equal. She believes that social, economic, academic, and ethnic factors do not matter. She says this in reply to the discussion that she and Jem were having. The exact quote is "there's only one kind of folks. Folks."