According to the Wikipedia article, in the song she identifies herself as one. However, she redefines the word not necessary about the colour of the skin, but also about the way of life of someone that is outcast from the society.
She is credited in the writing of the lyrics so the choice of this word was intentional.
It did become a problem to the point of the song was not aired in radio. The book
White Riot: Punk Rock and the Politics of Race by Stephen Duncombe and Maxwell Tremblay says:
Because the Night (...) became Patti Smith's most popular song. Rock N Roll Nigger, on the other hand, couldn't even be played on mainstream radio.