Apple can (in theory) validate that the things going through the app store aren't total malware. In-browser? You're on your own, for good or for bad.
They took it very seriously, as well they should. It was clear that mobile, even then, was going to become so big as to start directing change on the desktop. If Flash is left out of mobile, Adobe's relevance is seriously threatened.
That said, I think the 'personal' nature of their response is just posturing. They're taking a victim stance to stir up sympathy because, well, they can. The press will respond to that story far more readily than a straight technological disagreement. And boy have they. It's confusing the issue long enough for Adobe to adapt their authoring tools to kick out competent HTML5, which will protect their revenue stream in either case.
What's more, Adobe would never have put this much effort into making Flash suck less on mobile platforms if Apple had decided that shitty Flash was better than no Flash and went ahead and shipped it with iOS.