The reality is that bad calls are inevitable in sports... period. Just google 2011 bad nfl calls, or go to youtube, and you will find numerous examples like this one.
NFL admits bad spot gave 49ers five free yards | ProFootballTalk
The difference this year is that you have numerous people (most who also happen to be union members or sympathetic to union members) who are overtly trying to make this an issue. I have a harder time watching games this year because of having to listen to announcer comments... not because of the refs.
Someone correct me if I am wrong, but thought I'd also heard that the refs in the replay booths are the official reps (not temps). If so... shouldn't these "bad calls" have been overturned if they were that bad? Or, perhaps, they also have an agenda in letting the calls stand.