Not that there was much ambiguity in Apple's position on Flash and Adobe, but just in case it wasn't crystal-clear to you, read Steve Jobs' Thoughts on Flash.
My conclusions:
There is a great opportunity here for Adobe, if they can move fast enough to take advantage of it (not their strong point): we need a great authoring tool for interactive HTML/JavaScript experiences. An evolution of the Flash authoring environment into an HTML5/JavaScript authoring environment could be the answer, and no doubt something like this is already in the works. If Adobe does this quickly, it could be a big opportunity. If not, someone else will step in.
See also:
Update: Adobe has begun an ad campaign and added a section to its site, with the theme We Love Choice. Pulling out its own celebrities to counter Jobs, the site includes an article titled Our thoughts on open markets by company cofounders John Warnock and Chuck Geschke.