I yield to no one in my partisan criticism of the NYT, but the failure here is likely not "we can't offend our corporate overlords" so much as it is "we don't have a single reporter on staff qualified to understand what was happening here." There are three options for getting stories: running them down yourself, following up on other reporters' work, and being leaked the story by someone wanting to do damage to someone else. For huge swathes of the human experience, the NYT just lacks the expertise to accomplish door #1.

This is the same reason why the NYT didn't break ScamVille, despite having published press releases about it. They simply don't have anyone on staff who understands affiliate marketing, Internet advertising more complicated than their own brand ads, social media ("sure sounds sexy though!"), etc.

The incentive structure in traditional journalism is a) have a big enough megaphone to get leakers to come to you and b) get good at owning the stories that other papers break while defending your own stories. Note that "get really good at breaking stuff" is much, much harder. This is why you'll see more and more bloggers with deep, deep talents in narrow fields break things in the coming years.

(One example: CBS got into a flap about the authenticity of some papers purporting to demonstrate something negative about George Bush a few years ago, and stuck to their guns about them. Then a cycling blogger who -- random hobby time -- also happened to be an expert in computer fontsetting realized it was impossible to produce the papers on the typewriters available at the time and, in a visual which should have won him a Pulitzer, created an animated GIF switching between frames scanned from the purportedly typewritten document and the same text typed into the default settings of MS Word, showing they were pixel-wise identical except for scanning artifacts.)