I don’t think Apple even dreams of a Windows-like share of the mobile market. Microsoft’s mantra was (and remains) “Windows everywhere”. Apple doesn’t want everywhere, they just want everywhere good. The idea though, is to establish the Cocoa Touch APIs and the App Store as a de facto standard for mobile apps — huge share of both developers and users.
So what Apple does not want is for some other company to establish a de facto standard software platform on top of Cocoa Touch. Not Adobe’s Flash. Not .NET (through MonoTouch). If that were to happen, there’s no lock-in advantage. If, say, a mobile Flash software platform — which encompassed multiple lower-level platforms, running on iPhone, Android, Windows Phone 7, and BlackBerry — were established, that app market would not give people a reason to prefer the iPhone.
And, obviously, such a meta-platform would be out of Apple’s control. Consider a world where some other company’s cross-platform toolkit proved wildly popular. Then Apple releases major new features to iPhone OS, and that other company’s toolkit is slow to adopt them. At that point, it’s the other company that controls when third-party apps can make use of these features.
So from Apple’s perspective, changing the iPhone Developer Program License Agreement to prohibit the use of things like Flash CS5 and MonoTouch to create iPhone apps makes complete sense. I’m not saying you have to like this. I’m not arguing that it’s anything other than ruthless competitiveness. I’m not arguing (up to this point) that it benefits anyone other than Apple itself. I’m just arguing that it makes sense from Apple’s perspective — and it was Apple’s decision to make.