I think the heart of problem is ads on NYTimes.com are exactly the same in the minds of marketers as ads on any other website, and that type of web traffic is just not that valuable.

In print, big media brands can use their brand value to drive rates up, which is why you see companies use "see our ad in The New York Times, Time magazine, etc). They need to find a way to leverage that brand value online, or maybe we're just seeing the death of a business model.