This word may have been derived from Spanish negro ('black' or 'black person'), possibly via British English or Dutch, which until very recently had neger as the neutral word for a dark-skinned person, or more specifically, a person of Bantu descent. The Spanish form is derived from Latin niger ('black', 'dark').

It's an unfortunate fact of life that perfectly clear and useful words can become laden with connotations and become tainted and suspect for that reason alone. This is probably what happened to 'nigger', too.