To be specific- you can use "nie" in other places, but then it means negation of that particular word
Dlaczego on nie kocha mnie - why he doesnt love me
Dlaczego on kocha ją, nie mnie, why he loves her, not me
....is the emphasis not on the word 'mnie' in this sentence anyway, in other words, ad one might say in English, "The operative word being "me"! Just dont get it, and its putting me off my learning!