Because that leads to exactly what we have now...using Flash for video. And a private company isn't going to cater to every niche platform/architecture.
Also, it's still left to the browser to implement. What specifying a format in the HTML5 standard does is allow the browsers to actually implement the feature since it gives them something concrete to reliably settle on. With HTML5 in all the major browsers, webmasters will then know they have another option that is widely available. This allows them to switch their video over to Theora|H264 and using the VIDEO tag, without worrying about isolating any users and knowing a wider array of devices will be supported.
As it stands now, for most web video you have to hope Adobe cares about your particular OS/Platform enough to cater to it (or that your platform will even let you use it, a la iPhone) . With an alternative standard implemented then all you have to worry about is if your browser, of which there are many to choose from, supports HTML5. There is no worrying about a private third party plugin that also comes with a fair amount of security holes.