I recently comped out booking an onsite room and 'gate price' tickets separately vs a package and for two of us it was actually $65.00 MORE to book the package thru Disney than if we had booked the hotel and tickets separately thru Disney. It's even more of a savings if you get your tix through LMT. That additional $65.00 gets you pins, lanyards, a ride pic, and a coupon book. In our case it also got us a backpack.
I think it's just the convenience of doing it all with one call or one 'click' that keeps people booking through Disney. I also think you get better customer service if you book through Disney and have special requests or need something extra.