"This isn't the slam-dunk negative article it's being painted as. As far as I can see, it expresses reasonable concerns about the war. I've read more pessimistic things. And more optimistic."

I would agree.
I would say that for NYT it's a balanced story- though not a "good" story in that will cause as much excitement. In general, getting view from some soldiers helps the NYT in terms of being seen as credible or serious- I think more stories like this would a good thing.

For details [color] and perhaps it could seen as more pessimistic, I recommend Totten recent piece:
http://michaeltotten.com/
Called "Balance of Terror" :

"“We aren’t being attacked because the Mahdi Army is in the next building,” he said. “They don’t want to hit their own people.”

American soldiers from the 82nd Airborne Division shared the small outpost with Iraqi Army soldiers who lived, worked, and slept in the building next door.

“You mean the Iraqi Army unit here has been infiltrated?” I said.

He nodded grimly and took a pull from his cigarette.

"That's a bad reason for us not to be mortared," I said.

"Yeah," he said and laughed. It was obvious, though, that he did not think it was funny. "
...
"Meanwhile, or at least so it appeared, I was safer at that outpost because the Mahdi Army was there. They did not want to hurt their own people with rockets and mortars. Moqtada al Sadr’s infiltrators and sympathizers enveloped me in a force field.

Iraq is a strange country. Where else can American civilians like me be protected by terrorist human shields?"