Where The Sun Don't Shine
But I think the accusation that the paper gave MoveOn a discounted rate because it's owners and staff like the ad so much is mostly a distraction. Ad discount rates are available to anyone savvy and knowledgeable enough to get them.
There are better criticisms to be made of the Times taking the ad in the first place. One of them is that it attacks the patriotism of an American military leader in the field.
The First Amendment doesn't require the NYT or any newspaper to make money off the slanderous ravings of a far left-wing, anti-US military hate group, any more than it requires any newspaper from accepting ads paid for by Osama bin Laden.
When New York City was offered $10 million from a Saudi prince after 9/11, then mayor Rudy Guiliani told him where to stick it.
That's what the Times should have told MoveOn.org to do with their despicable attack ad along with all the money they offered them to run it.
UPDATE: Then again maybe NYT's politics did have something to do with the ad and the rate quote after all.