Microsoft definitely has their own crazy and draconian licensing and "ownership" issues, but I can't tell from your comment which one of the thousands of possible example cases you're referring to.
If you have a well-reasoned counterpoint, please post it. I'd honestly love to hear a different perspective.
If I understand correctly, you argue that users don't "own" the device because Apple sells it as a whole stack or because they write the iOS and license it to users. My point is that even with licensed OS users should be free to do whatever they want on the device. When I buy an iPhone, the iOS is already installed so I assume I have also bought the right to use it (like Mac OS?). It doesn't matter whether the OS that comes with the device is written by the hardware manufacturer or not; hence the Microsoft analogy and that's why i disagree with you.
Now when it comes to the subject of App Store, someone has pointed out correctly that App Store is a distribution channel and Windows or iOS is an operating system. It was not my comparison. Here I do agree that Apple has every right to charge developers for any amount they want, or the right to deny any app they don't see fit in the App Store. However Apple don't allow any other channels on their system. That is still in their right to do so, but it will raise some issues when the iPhone/iPod Touch reaches a certain market share.
A better example would be Google. What would happen if Google tried to own some of the dollars that flow through the organic search channel? /shudder
It is a pretty good comparison as long as App Store is the only way to install anything on iOS
It may strike you as obviously false, and it may well have been so two years ago, but when I got my new iPad after moving to another country I've spent about twice as much time getting iTunes to let me pay for apps in foreign App Store than I've spent researching jailbreak options and caveats and then actually pwning the device.
So no, App Store is far from the only way to distribute iOS software, even though it still is the default and sometimes the only apparent way.
From my experience, it turns older iPhones into a stuttering laggy mess and breaks visual voicemail, and makes you paranoid about every iTunes update.