I do think that there are some technical concerns that Apple has rightly presented. I don't see a point of presenting them yet again - we all know what they are, and we either agree that they are real or we don't. Never mind.
I have consistently argued that Apple's position is philosophical. Their decision not to support plugins like Flash, Silverlight, and Active-X stems from their desire to create the principle duality on their platform between open and closed, between unmanaged and managed.
Apple has consistently articulated that they believe in their closed, curated platform because it provides a better user experience; however, they have also said that they fully support the open web. But, instead of defining the open web as some sort of abstraction, Apple has chose to define it specifically as what the W3 supports.
The W3 endorses javascript, CSS3, and HTML5. The reason that Apple supports the W3 is two-fold. Namely, these open ensures users enjoy a consistent experience, and also that the tools of web development are always democratized and accessible. No one company, entity, corporation, trust, or otherwise, controls the creation or distribution of content. It really is a beautiful thing. Furthermore, Apple can help to improve the W3 and the open web, as it has by contributing WebKit. Apple has no influence over Adobe - nor does anyone else, which is precisely why Flash is diametrically opposed to everything the W3 stands for.
Flash, Silverlight, and Active-X all fundamentally and undeniably violate the principle of the open internet. That is NOT to say that they are not useful, and that developers cannot use them to do amazing things. But that doesn't change the fact that plugins violate the open web in the most basic philosophical sense. While Flash, Silverlight, and Active-X should and are used for niche products, they should not be considered part of the open web. If developers choose to use these proprietary technologies, then they will have to weigh the benefits and determents accordingly. There is no expectation, nor should there be any expectation, that these proprietary plugins becomes standards.
This issue really has nothing to do with Apple. Apple chose to support the W3, and to clearly articulate what they believe the open web to mean. If you are of the persuasion that Adobe Flash should be part of the open web, then your issue is between Adobe and the W3. It's not about Apple at all.