They are making money from the ecosystem of developers & content separately. Why should it be counted in the price of the phone? Secondly, I didn't discount the quality/design from the phone price.
Apple doesn't just overcharge for additional flash, they overcharge at every possible item in your phone. Example : $30 cables/connectors/chargers. On top of that, they sell you last years model at a premium too. Up until a few months, they were selling iPad 2 at some ridiculous price. The BOM cost goes down significantly with new rev of components coming out, be it the camera module, the previous generation app processor, the foundry charges, the low res LCD,...