You were able to watch Hulu on your iPad, but, unless I miss my guess, you were not able to play Flash content on your iPad, but rather streamed the Hulu content from somewhere else.
From following a lot of Mac-focused news, I get the impression that Flash has never worked as well on a Mac as it has on a PC. I think that's part of the reason it wasn't included as an option in iOS. And I really don't hear as much clamoring for Flash as you would think. Most websites want their content accessible on iOS devices and make the necessary changes. The ones that do not seem to be those without the resources to recreate their sites in an non-Flash format, and Hulu, which is turning it's Flash-only website into a way to make more more money by charging iOS users to access Hulu.
You're right in that something is going to have to change. If non-Apple tablets take off, and if Flash support is cited heavily as a reason for choosing a non-Apple tablet, Apple may have to cave. But if that doesn't happen, then Hulu will be in a position of doing what will be seen as punishing iOS users by making them pay a subscription fee while other tablet owners access the web site for free. That's probably not going to go over well, either, and I wouldn't be surprised if Hulu was the one to eventually cave. They seem to make their money from advertising, which means more eyeballs=more money. If Apple continues to be a major player in mobile devices, Hulu is simply going to have to find a way to support the iPad without Flash, just like most other major websites are.
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