It's not unusual in sports or life in general for one person to get punished for breaking the law (or league rule) even though others have done it before them. No court in the land will accept the "yeah, but other people do it too" defense when someone has been found committing a crime.
I've heard that argument before, but the thought that the league is somehow targeting the Patriots seems absurd when you think about how successful that team has been and how much it means to the league. If anything I'll bet they had tons of internal discussions about this, wondering how they were going to actually "prosecute" the golden child. But in the end they decided they had to show that even the golden child can't get away with cheating. They went easy on Belichik for the videos of other teams walk-throughs and they knew they couldn't look the other way again.