Here's an interesting theory:
Glad you commented on this NYT story, because it’s been baffling me as well, but you didn't mention what I think is the most bizarre aspect of this story, which is that it this story in fact makes the administration look great. It's a legal and intelligent way to be tracking terrorist activities at home and abroad, and I think Americans would be more shocked to discover that they weren't doing this.
If this had been reported by Fox News, it would likely have been dismissed by most as simple conservative media cheerleading. So how’s this for a conspiracy theory? The administration wanted this story to be leaked, and they wanted it to be leaked to the Times. That way they get to a) trumpet what a brilliant job they're doing fighting the war on terror and b) vilify the Times and the press, which is always good for firing up their conservative base. I think this was Bush and Rove at their finest, and Keller got taken for a ride.
The blogosphere played its part as well, I suppose. And who needs Tony Snow when you've got Instapundit?