Actually, that's a great question. I was wondering that myself. Obviously the old school, superstious pirates like Gibbs believe that women are bad luck aboard ships. Which is strange, since ships are reffered to as being feminine.
Though, I think it's a tribute to Elizabeth that Gibbs is willing to make an exception of his opinion for Elizabeth. I've been noticing how much of an intricate part of the crew she is. Jack gives an order, Elizabeth is quick to take up the call. Also, besides Gibbs, she is one of the few crew members who stands on the upper part of the ship where the wheel is. (My knowledge of ship terminology is woefully limited).
Here's what I found out about the pirate superstitions:
Women onboard a ship make the sea angry.
If you come across a bare footed women on your way to a ship, bad luck would be sure to follow.
A naked women onboard a ship calms the sea
Hence the numerous bare breasted figureheads on sailing ships of old. Who ever said a sailor was politically correct
Also it says that it's bad luck to rename a ship....The original name of the Black Pearl is the Wicked Wench. Maybe that explains why Jack has had some bad luck with the ship...