Well, I haven't watched the VOY series yet, so I will not say anything about Janeway. However, when it comes to female bosses, that is an interesting dynamic. If you are the (male) flea under the foot of the boss, and the evil manager is an attractive woman, there is the attraction element which always fights with the desire to escape the great evil that is haunting your very life. It adds a terrifying psychological part to an otherwise inappropriate crush.
As for the OP's dad, I kind of rank him in a separate category. Some people really get a kick out of gay jokes, and for him, it is probably just as simple as that. The very fact that the character on screen isn't sleeping with dudes frequently and is seen around other women is taken as proof enough that there is something strange going on.
In any case, one vital part of romanticism is the male desire to protect a woman (Think The Menagerie
) which is clearly not there if said woman outranks him and is giving orders. I wouldn't say that a woman being boss eliminates her femininity as a whole, but it probably does for those who are below her in rank.