In six cruises we have missed two ports, both due to rough seas. The first was Costa Maya and we missed the Mayan ruins, the second was last year we missed Half Moon Cay which was one of the main reasons we chose that cruise. It really stinks when you have an excursion planned, it is a sunny day and you can see your destination!
We made the most of the cruises anyway and as always had a great time. You can understand the Captains decision as safety is always first, but then you wish that the would build a harbor or breakwater.