kpgclark,
We have Disney book the air for several of reasons. Mostly for the convenience. I did some research and figured that I could save less than $100 total for two people if I booked the air and hotel by myself, depending on the time of year and the current airfare. It is more convenient for us to fly out of Ontario, CA than LAX, but that makes air more expensive. I could have saved money if we flew out of LAX on our own, but not really a great deal flying out of ONT. We also like staying at the Hyatt because it's convenient. I don't want to have to wait for a shuttle to another hotel after just spending the whole day on a plane. We can be checked into the Hyatt and in the pool within about 20 minutes of claiming our luggage. With the air program, the cruise line will collect your luggage outside your door at the Hyatt on the morning of the cruise, and deliver it to your stateroom. So you really only have to transport your luggage from the baggage claim to the front desk of the Hyatt. Finally, as has been mentioned before, if DCL books your air, they are responsible for making sure you reach the ship, or getting you to the next port. This isn't such a big deal when you arrive the day before, but if the ship is late returning and you miss your flight, they're also responsible for re-booking you.
So yes, you can save money by booking your own air, but in our case, we feel that the extra we pay for our situation is worth the convenience and peace of mind.