small discounts..
Discounts may be small, but its entirely possible that that 5-6% is all the profit that Amazon make from selling them. If you've ever worked in a retails shop (other than apple) who offeres staff discounts, they almost always exclude apple products.
Apple buyers tend to spend a fair ammount of money on accessories for their iPhone, iPad, iPod, Mac etc, which is where the retails will make their products. Most of these accessories will be costing less than 1/3 of the retail price.