OK, that makes sense. But if Apple does the same to Amazon or Netflix I can see them going the web app route if they are not allowed to raise prices, because it would eat all their profits, too. Amazon has already showed a web app version of their store, and Netflix is experienced with HTML5, too.
Amazon was working on the HTML5 version well before this decision came about (they previewed it during the Chrome Web Store launch). What they showed doesn't looked optimized for touch use. That could change, of course. I imagine their strategy is to stay quiet and hope Apple doesn't go after them; and when/if that happens they'll adjust. They could be one of the few companies capable of eating the cost to stay on the platform but that would mean strengthening a direct competitor. I'm very interested to see how they handle it.
As for Netflix.. if you're talking about their HTML5 player that was in the news a few days ago to be on Chrome OS, that requires a plugin. <video> doesn't support DRM -- and never will/can. I think Netflix may be the one company that is given an exception due to their influence over Apple TV sales.