The main problem has been that until recently there were no decent multimedia content creation tools apart from Flash. So if you were developing for a website and wanted rich multimedia content, you didn't have much choice. Tumult changed all that with Hype, which started off tentatively but has developed into an amazing content creator that's entirely HTML5-based. It can do much of what Flash could, but in a much more intuitive interface.Flash should have died with the emergence of HTML5. I'm surprised it's made it this far.
I knew that Flash's days were over when Media Boom converted their entire site to HTML5. They used to be fully entrenched in Flash and it must have taken them a lot of work (and money) to make the change. But their efforts have paid off.