Yes, they are real employees. If I remember correctly, those commercials were filmed at ORD over a two or three day period a couple of weeks after the 11th.
After I posted my first response, I started thinking a little more about those spots - Its not the employees I mind so much, its the way the commercial was filmed. I thought the days of the camera constantly moving around were over. That element annoys me, but I guess you've also got to remember that the employees in these spots aren't behind the camera, setting up the shots and shaking the camera around, and they don't pick which segments get aired and when. Those decisions are made by an ad agency. I guess what I'm saying is that we can easily make fun of these people, but they're real people, the ones on the front lines trying to keep the airline from becoming another sad chapter in US aviation history. So I'm going to give them credit for backing up their jobs and their airline. Yep, even if they do fly strange aircraft types.