Needless to say none of the cruise lines will put passengers, crew or ship in jeopardy when storms are brewing. If there is something in the Gulf of Mexico or threatening Jamaica, Cayman Islands, or Mexico, they normally change and do an Eastern Itinerary and vica versa.
But now, we have Gustav heading into the Gulf and Hanna playing around and growing east of the Leeward Islands (supposed to follow Gustav maybe and loop around to Cuba and west and then north into the Gulf.
So this is a great question! With the sophisticated sattelite information and the flexibility to move ships as necessary, somehow they can travel around and get behind storms or out far enough in front to head to where the storm already passed through. Either way, they do seem to keep ships out of harm's way. Maybe a or several ports are useless (damage etc.) so they can't stop there, but there is so much to do on the ship anyway----------- but that's another topic.
Gustav and Hannah are sure making life interesting right now for the cruise lines and I'm sure glad I'm not the one trying to figure it out and make it all work. Living here in FL, hurricanes are always a concern but we have never not felt safe being on a ship (and love to cruise during hurricane season). I actually think of them as great hurricane shelters - bars, food, entertainment and activities (hot water and electricity too
So the answer to the question is somewhere safe, you can bet on that.