In my experience, the difference comes down to the level of service you're looking for, in other words whether you like to have total control or prefer to let someone else do all the legwork for you. If you aren't familiar with the different resorts, types of tickets, dining options, etc. and aren't the type to want to research all that yourself, then a travel agent is perfect because they can answer all your questions, suggest what's best for your needs and then make the reservations for you.
That being said, the CM's at the Disney Travel Company are very knowledgeable, friendly and helpful and can answer all your questions as well. So, if you like having control and being able to make changes yourself, this is a better way to go. We always make our reservations online ourselves and then call the DTC for any extra help we need. They've always been great and I like not having a middle man.
As for savings, I don't think there really is much. We're going later this month with some family friends, and they used a travel, we didn't. We both got the exact same deal, but any time she wants to make an adjustment to her reservation, she has to leave a message for the travel agent and wait for a call back. I just call Disney
