"Namely, we're finally getting to the point where developing Windows only apps is no longer viable."

There's no story here. Both Silverlight and AIR are cross-platform. NYT chose AIR over Silverlight for purely technical reasons that all seem reasonable. Silverlight is not as far along as AIR at this point, simple as that.

The article mentions a bunch of anti-Microsoft comments on the NYT web site, suggesting that 'Microsoft-rejection' led to the migration to AIR. I find that very unlikely.