Making money is their MO. It comes down to simple supply and demand, and it makes prefect sense to raise their prices slowly overtime.
My money is on Amazon doing what they have always done: compete with wide selections and the cheapest pricing possible while using Whole Foods to bring their Fresh delivery service to far more markets at a higher efficiency.
I would have done this with Peapod etc but their website was lacking in 1) choices (Amazon will get you pretty much any food item) and 2) delivery window and 3) unattended delivery