This topic is beaten to death whenever he calls our games.
My thoughts? He goes out of his way to not sound like a Cowboy homer. That's just my opinion. He's such a perfectionist at everything he does, and he realizes that everyone sees him as a "Cowboy." Therefore, he's worried that if he takes the Cowboys' side on too many issues, regular fans will see him as a mere Cowboy homer and not take him seriously.
Now, that's just my theory on the whole ordeal. Yeah, I agree he sometimes sounds overly negative. But, at the same time, we haven't exactly been good since he retired. Secondly, nothing he does or says in the booth will ever diminish his accomplishments on the field for this franchise.
Frankly, he won us three Super Bowls. He can now say whatever the hell he wants to.