Much of the original reason for Hulu's creation was frustration on the part of NBC and Fox executives. They wanted more control over their content than was offered by services like YouTube.
When Boxee users were suddenly cut off in February Hulu CEO Jason Kilar made it clear the decision came from those rather than Hulu management. Since then Hulu's ownership group has expanded to include Disney, a company known for their near-paranoid attitudes when it comes to content control.
Hulu desktop appears more like an attempt to create their own Boxee alternative. A message warning Apple users to shut down Boxee so their remotes will work correctly seems to confirm this.
When Hulu initially launched the only major streaming video player was YouTube. One of Hulu's advantages was being designed around professional content instead of user supplied video.
With support for numerous online video and audio sources, Boxee seems better suited to serve viewers' needs than a single service client like Hulu Desktop.