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You are thinking of the term "son-of-a-bitch" (a term that is almost never directed at a person these days). The term motherfucker doesn't imply anything about a person's mother (and it never has), unless you call me a motherfucker, and attribute that to mean that my son's mother gets fucked in the good way.
I always felt great whenever I was called a motherfucker by either a man or a woman. Being a bad ass motherfucker, or B A M, is a good thing. Just ask Samuel L Jackson.