I think the bottom line here is to do what you're most comfortable with. I am of the mindset that I would rather make my reservations thru a travel agent as it keeps local businesses in business. Disney still gets the majority of the money anyway, as agents only make a small % of your total vacation package.
The key is to be sure you're 100% comfortable with a travel agent. Ask if they've been to Disney and when their most recent trip was. Ask what hotels they've stayed at (onsite AND offsite) and if they've ever used a Dining Plan, done
MVMCP, etc., just to be sure they're not just saying "Oh, sure, I've been there before." Does the agent get excited when talking about Disney? Does the agent start giving you little tips and tricks right away? All signs of a really good agent who knows their stuff when it comes to Disney.
A good travel agent will keep an eye out for all of the sales Disney releases and will re-book you under that promotion so you're never stuck paying the higher rate.
Contrary to what other posters have said, the reservation DOES "belong" to you. The travel agent will give you either a 12 digit or 8 digit/letter WDW confirmation # so you can log onto Disney.com, enter in your confirmation # and pull up all of your information. So you can make dining reservations, etc. Even if you wanted to make changes to your overall reservation (change hotels, change room categories, etc.) you have to call Disney direct. All you have to do is call your travel agent and s/he will do all of the calling for you.
I honestly see no downside in booking with a GOOD, knowledgeable travel agent.