There has been lots of chatter lately about how "The Internet" has voted for Conan O'Brien. Sadly for Conan, Internet chatter doesn't pay the bills at the TV networks, and neither can it threaten to scuttle the NBCU/Comcast deal.
In the battle of Jay vs. Conan, the end of "Conan at 11:35" might have been prevented had viewers actually watched his show. Had Conan been pulling better ratings at 11:35, NBC may very well have given Jay the heave ho at this point, instead of effectively giving it to Conan.
The chart above tracks the weekly ratings for The Tonight Show and Letterman's Late Show since Conan took over through the week ending 1/1/10 Chart updated to include ratings through 1/8/10. While week to week variations are often explained by repeat runs, the overall trend is clear. After trailing Leno's Tonight Show for nearly a generation, Letterman closed the 18-49 demo gap with Conan in early fall and things have been neck and neck since then.
While I am sympathetic to arguments like "Conan wasn't given a chance", "Leno took all the guests and killed 10pm ratings", and "Conan didn't have enough time", clearly NBC was not.
The NBC affiliates presumably forced a move right now, and Conan was left with the short end of the stick. That might have been different if all the members of "Team Conan" had actually watched his show.