The author explains that Flash breaks 3 fundamentals:
* it encourages design abuse
* it breaks with the Web's fundamental interaction principles
* it distracts attention from the site's core value.
Anyone who implements a fancy custom scrollbar, forgets an ALT attribute, or doesn't properly wrap their label tags is breaking these fundamentals all the same.
It's not like I don't agree that Flash could be better, but this argument could be applied to just about any technology at any point in time.