I don't have a good explanation for that. Before I go any further, I should point out that there is plenty of positive stuff said and written about the Patriots. I just seem to remember the negative stuff a lot clearer.
As far as why the media went with a lopsided reaction to the sideline signal taping, three possibilities came to mind, but only the last one might have some truth to it: (1) All the negative stories about the Patriots are true. They're really destroying the integrity of the game. (2) There's a vast anti-Patriots media conspiracy. (3) The media has figured out that negative Patriots stories get a lot more traffic than even-handed stories.
The media has access to more people and information than the fans, so you would think they could produce more nuanced thoughts on situations the Patriots have been involved this year and in 2007. Instead, they try to portray the story in a simpler good/bad, black and white frame.
The article linked by the OP is a good example. Over the course of 10 months, Clayton completely changed his opinion on stealing signals without any explanation. Back when the fake story about the Rams Walkthrough was going strong, John Czarnecki, who was with Fox Sports at the time, wrote that he was on the field during the walkthrough and it wasn't a very intense or organized event. He was the only one to say something like that, but I doubt he was the only media member present that day. Or even if they weren't at the Rams walkthough that year, I find it hard to believe that, for example, Peter King or Don Banks never attended one. They could have offered some insight on whether teams took it seriously or not. Somewhere in the deflate-gate forum there a thread about Boomer Esiason, where Boomer says there's a lot of petty backstabbing in the league, ‘You want to call me out? I’m going to call you out. You want to embarrass me? Guess what I’m going to embarrass you.’ - kind of stuff. He only mentioned this after the SB, but former coaches and players and some of the media had to know things like this happen in the league. None of them mentioned this might be that kind of situation that blew up on the Monday after the AFCCG, though. Along those lines, Palm Beach Pats Fan wrote about a recent conversation he had with a NFL referee. The referee said that a lot of the complaints they hear are groundless and just based on the paranoia of highly competitive coaches. Others are minor incidents that the league deals with quietly. Less often, there's a real problem that makes the news. Again, some people in the media had to have heard similar versions of this from other officials, but if any of them were thinking along those lines with the ball deflation story, they were in the minority.
