I think this right here is the most honest reason Jobs actually gave:

This becomes even worse if the third party is supplying a cross platform development tool. The third party may not adopt enhancements from one platform unless they are available on all of their supported platforms. Hence developers only have access to the lowest common denominator set of features. Again, we cannot accept an outcome where developers are blocked from using our innovations and enhancements because they are not available on our competitor’s platforms.
That's sounds good and logical, right? But that is the exact same logic that played a huge role in damning the Mac to baby brother ~5% market share. Yes, there are downsides to making your platform support software that is cross platform. But the upsides are HUGE. Among other things, it means your customers actually get some CHOICE in how they want to use the device they bought from you.

But Apple has NEVER liked for people to have choice. Whether its printers for their Macs or software for their iPhone.

Flash is a cross platform development tool. It is not Adobe’s goal to help developers write the best iPhone, iPod and iPad apps. It is their goal to help developers write cross platform apps. And Adobe has been painfully slow to adopt enhancements to Apple’s platforms.
There you go.