That would be a valid point if the phone wasn't vertically integrated with cloud services and ongoing support from the manufacturer.
The terms for access to the app store are based on licensing for the software that's part of the device. I could see a reasonable compromise where you can wipe the iPhone and start from scratch with your own OS/drivers/etc, waive your warranty, and then be free to go nuts installing anything you want from any app store. I just can't imagine anyone being happy spending the thousand bucks purely for the hardware.
The infrastructure is already paid for. I paid for it when I bought my $1000 iPhone.