We're DVC members, so we always end up doing our own WDW bookings around our cruises. As far as I'm aware, the only thing you can't get booking it yourself is your hotel and stateroom keys combined into one! You also have to check in at the port, rather than being checked into your cruise when you get to your resort.
Otherwise, you can get the same price on Disney transfers and probably a better deal on air as well as your hotel doing it yourself. Plus, if you look at towncars or one-way rentals, you may be able to save on transportation as well. On our last cruise, we did 2 1-way rentals with Budget and saved about $50 over the cost of
DCL transfers for 3. That's $50 more to spend on the ship!
Amanda