I was also under that impression, but Shuttle does a LOT of hub to hub. UAL jumpseaters have told me that the prohibition of which you speak was either a company proposal that was made during contract negotiations which didn't make it into the final deal, or might be part of an allowed percentage.

I found it a little amusing that a UAL executive actually used EWR-IAH (a route that Shuttle regularly flies) as an example of the type of domestic route UAL plans to fly with their 777-200s.