I'd always assumed that buying airfare on my own would be best. I'm still pretty much in agreement with this, but let me share with you my most recent experience.
My wife and I did TONS of research on airfares, and were flexible as far as airport, time of day, and even which days to fly (6 or 7 days within a 12-day window). We found the best fare/airline/airport/date combination for us. With that in mind, I called Disney to tweak my reservation to match the date swe'd be flying. The rep asked if we'd already bought airfare, I told her I was about to, and she asked if she could check into it for me. I gave her the dates and flight numbers, and she came back with a quote that was something like $120 cheaper PER TICKET than AirTran's own website. Disney got me on AirTran for almost $500 cheaper than AirTran would have, for the 3exact same flight. I don't know if lightning will ever strike a second time, but you're darn tootin' I'll be checking with Disney before booking airfare again.