A couple years ago I went on a Caribbean cruise in late September. It was hot & humid, and there were hurricanes going on (3 of them) but we were nowhere near any of them and had no problem. Last year some friends of mine got a free extra cruise night when one of the hurricanes kept them from getting back to Miami on schedule. Fortunately their TA was able to get their flights rebooked for the next day!
One big advantage of cruising during hurricane season is that ships will do almost anything to avoid getting caught in the storm - changing itineraries, skipping scheduled ports of call, staying out longer or going back to port earlier if need be. (They will usually compensate their passengers to some extent when cruises are shortened due to weather or technical problems.) If you were at an island resort, you'd either be stuck there during the hurricane, or would have to leave early.
I'd recommend going for it - relax & enjoy, knowing the captain will not put you in danger!