User annotations help make the user feel they are part of the community/creative process. Walled gardens like NYTimes might be scared (remember ThirdVoice) to let the public annotate their content - highlighting is a trojan horse to overlaying user annotations and co-opting their precious content. If I were the NYTimes, I'd be scared to sign any revenue-sharing contract unless it specifically prohibited later, more sophisticated annotations.

One of the most-popular sites in Japan is a clever site that lets anyone comment directly on a video, literally.

http://en.wikipedia.org/wiki/Nico_Nico_Douga