Well, it's free to read the website and they haven't quite figured out how to make much on the ads. It's extremely difficult to make enough money off ads to support a world-class team of reporters (or even just a world-class web team!)

People have written many books on this stuff, but I personally don't think it's even possible to make as much off ads online as they used to make off print a few decades. On top of that, the NYTimes biggest advertisers used to be national retailers, auto retailers, real estate, and finance companies. Those also happen to be the sectors hardest hit by the current recession.