First: Earth Starfleet is not the same organization as the Federation Starfleet. The latter is military; the former is not. So protocol is likely to be different.
Second: Of course Janeway doesn't like to be called 'Sir'. Janeway is female! Sir is a male term. You want to talk to a female superior officer, call her "ma'am", because it bloody well makes logical sense. People outside the military use the word "ma'am", so why shouldn't they use it IN the military?
Third: Strange as it may seem, there are - or were, I don't know if this shit still goes on - some extremely radical feminist groups who make up words like "womyn" and "herstory" because they don't like any word with "man" or "his" in it.