went to whitsundays december last year, price-wise wasn't any different booking myself as opposed to using a travel agent. travel agents generally make things much easier, everything organised, they find the cheapest prices etc.
but honestly, i found the whitsundays extremely disappointing, and didn't see what the big deal was. sure the barrier reef is beautiful, but all the whitsunday islands look like dried up bushland surrounded by water. lot's of humidity, rain and mosquitoes.
but note - my previous holiday was in fiji, so my expectations were high. it was kind of like going to warner bros movie world after going to disneyland, major let down.