Of course a big part of this is Zynga bet huge on Flash (for no particularly good reason). If Zynga had bet on HTML5 it's stuff would all be working on iPhone for free.
Far be it from me to be someone who defends Zynga on anything, but your post is pretty ridiculous.
HTML5 is a pretty iffy target platform for games today. It is very difficult to support all the different browsers across desktop and mobile well and still have fast audio and even just simple 2D graphics. That's today.. in 2007 (when Zynga was started) HTML5 basically didn't exist as anything other than a pipe dream. If Zynga had "bet on HTML5" back in 2007 they would have been a stillborn company that never made any profit to begin with. For the types of games they make, Flash was inarguably the only option then and even today on desktop browsers it is arguably still the only reasonable option.
Yes, HTML5 will be great for games, maybe in 2014 or so. I'm sure they have people there working with HTML5 and getting ready for that.
I can't speak as a big Zynga user (indeed, I don't play their games at all) but my wife is a total addict. Zynga's games, as far as I can tell, and certainly the older games, don't make much use of capabilities that Flash offers over plain old HTML4 + JavaScript. So, in essence they picked Flash because it _might_ have let them make interesting games with what was at the time a ubiquitous engine, but in fact they made rather uninteresting games that could have been done without it, and this has cost them dearly.
Zynga used Flash for the same reason everyone else uses Flash -- ubiquity and consistency. HTML 5 canvas/JS would require divergent codepaths for each browser since they all implement different subsections of the spec (occasionally in different ways) and would still probably require a Flash fallback for IE users (most of Zynga's target audience).
It would be nice to get automatic compatibility with anything that runs a modern web browser, but the sad reality is that most PCs don't use a modern web browser, and HTML 5 doesn't really simplify anything. Flash runs the same everywhere from only one codebase.
I'm a big supporter of HTML5 and I strongly dislike Flash, by that's ludicrous. You can't just put a game designed for desktop/laptop screen sizes and for the mouse/keyboard and expect it to work as-is on the iPhone.
The game may load, but it won't be playable. You need to do a version for that type of UI. HTML5 would enable reuse of the backend, but not much more.
