The benefit to the transfer is that SOMETIMES the ship will wait for you if your plan happens to be late - especially if there are more than one person on the plane going on the cruise. And they also ensure that you have flight times that will make sure you dont miss the boat. Apparently, they will also pay for a night in a hotel in the embarkment city if they cant get you on a flight that will get you there early enough to catch the boat.
I personally wasnt able to book a flight with my cruise (something about the city I live in), so I am looking for cheap fare and planning on coming in a day early. I am usually great about finding flight deals, but havent had any luck so far. Another poster mentioned that b/c of increasing fuel prices, flight prices are higher than usual, which makes perfect sense.
So...basically after all this rambling - I would take the transfer if I were you. Let the cruiseline worry about getting you on a good flight.
Oh, they also will transfer your bags for you so that you dont have to go to baggage claim at the airport.
Hope that helps!