To put this story into context, remember that the biggest stake holders in Hulu are NBC Universal, Fox Entertainment, and Disney (27% each).
EDIT:
Hulu Desktop is at http://www.hulu.com/labs/hulu-desktop, have a look at the screenshots or try it.
Note that "Hulu Desktop will work with Apple and Windows Media Center remotes" suggesting they don't expect it to be driven by a mouse and keyboard.
If you're going to go to the trouble of distributing a desktop app, why the fuck would you still accept playback 100x crappier than native implementations?
Sure the folks building Hulu may feel that way but this is a business that's still figuring out how to do this in a way that works for everyone involved and right now TV ads are the cash cow for the networks.
From Hulu's perspective really the best thing to do right now is deploy their content in the most restrictive way possible because they don't want to identify a model that works and then be in a position of having to limit functionality or access to existing users in order to make it happen. Its always better to be able to add access then to take it away.