I, too, always book my WDW stays by phone instead of online. However, before calling, I check the fares so that I have a rough idea of flight times/pricing. In my experience, WDW has access to the same flights I can find online; however, like Cassie said, I have no idea what the markup might be (if there is one) on flights purchased through them.
One thing you can do is find a flight you like, then call WDW and ask them to price out your resort/dining/whatever without airfare and with airfare (the same flight you chose). See if there's a difference between what they offer and the price of purchasing your own tickets.
Of course, if you have airline miles or a discount code/offer for a flight, I would totally use that and NOT book through WDW.