As far as I can tell, those corporations have been using third party ad networks to serve ads on their web properties. I think that limits the amount of control the NYTimes or WSJ might have over the pricing of ads, since the same ad might be run on a high-status newspaper like Washington Post and also on middling web-only pages alike.
I'm sure there are anti-trust implications if done improperly. But "The Deck" advertising network works on the same principle: limit ads to a certain network of blogs with a certain type of content, charging a different rate, having control over the type of ads, and delivering a certain known target market to advertisers. My idea for the big news/media corps is essentially the same.
Those folks have been selling ads for some time. What evidence do you have that they're doing it (significantly) wrong?
Note that all of those publications are losing off-line subscribers like crazy and the on-line numbers aren't growing as fast.
Are there anti-trust implications in your proposal?