Why would they do what, exactly? Sell their phones? Of course they are going to sell their phones in their brick and mortar shops. Cook answered an interview question honestly. I mean when he sidesteps, people call him on it. When he answers a question point blank people look for ulterior motive. Until Apple decides their stores are nothing more than show rooms it makes absolute sense to sell their new products in store.
I see folks frustrated that these aren't ALL allocated to online stock. Why should a launch day item be restricted to online only orders? That completely screws some folks out of the IUP program, for example.