This comes up on the BattleTech side every now and then, the answer is in the past Amazon asked for a slice of the pie that was larger than others got for selling. The predicted volume of sales, combined with getting others (read: B&M stores) upset, was not considered worth it. That's why you rarely, if ever, saw Amazon selling BattleTech books under their own name. All the times I saw books listed they were either through an Amazon retailer, or with a lead time so far out that books were going through the general distribution channels and Amazon just ordered them like they were a regular store.
A position I agree with handily, by the way. Brick and mortar stores are how RPGs live and die. They are the last group that you want to have upset with you. But that's a topic for another day...or at the very least another thread.