Yes, since Carnival did the air they will be waiting for you and make every effort to avoid leaving without you. But only to a point. This is why it is NEVER a good idea to book a flight for the same day as the cruise....because something could happen (security event, weather, etc.) at your home airport, or really any other airport, which could delay your arrival at the cruise port. So if something happens which delays your arrival until 9pm for instance, the ship will be long gone.
Why did you go with the cruise line air? It is rarely cheaper than doing your own air, where you also have more control over the flight times.