Surprised people seem to forget that the NFL is really just 32 billionaires with big egos. It is only human nature for the other 31 owners to be a little jealous of the national attention the Cowboys get, win or lose. While they might like the business side Jerry brings to the NFL and the ratings Cowboys games bring which in turn brings big money, I'm sure most would love for Jerry and the Boys to taste a little humble pie and feel what it is like to be a normal team.
When the majority of the highest level of a company feels one way, I'd imagine it filters down to lower levels. I wouldn't be surprised if some refs can feel that hidden animosity of a majority of owners toward the Cowboys and subtly and maybe unconsciously call games with that in the back of their minds. It wouldn't shock me. Although no formal anti-Cowboy bias is out there I'm sure, the informal bias I'm sure is.
If you have 32 bosses and the vast majority you feel would like you to do things a certain way, you probably want to please them or what you perceive would please them.
So I think Drew is right. There is a concealed hate toward the "unfairness" of the popularity of the Cowboys by the other owners ( kind of like average/poor people often have toward the rich ). This would probably manifest itself through the lower echelons of the NFL, creating a bias against them.