The Commissioner sent out a league directive, warning teams they would be punished severely if they taped other team's signals. The Pats received such memo. The Pats violated such directive. They lost a first round pick because of it.
I'm not sure why people insist that the Pats didn't do anything wrong. It's understandable why this was a big story: the undefeated team, led by a coach that has a tendency to be a bit of a jerk, directly and knowingly violates a directive from the new disciplinarian Commissioner. The Commissioner thought it was a huge deal, by fining both the team and Belichek and taking away a #1. I don't blame the media for their reaction (except for Tomase, if he really did print that story without a reliable source).
The Donaghy thing got huge attention at the time. Since then, though, the FBI hasn't found any involvement from either other refs or the NBA itself. When allegations have been made (against Bavetta, against Foster), the media has reported it, but without proof, and without NBA action, it's hard for them to justify spending weeks on the same non-story.