It was anti-Pats because it was explicitly put in place because Bill Polian was tired of his Colts losing to the Patriots, and to combat what he thought was their defense of the time (2004). That part really isn’t debatable.
It wasn’t until 2007 that the Patriots began to make use of the change.
As for the roughing the passer, Brady is consistently in the bottom third of the league in receiving roughing the passer penalties.
I doubled-checked this. It was not a new rule, but a re-emphasis of the 1978 rule. The league admitted they missed 6 PI against NE in the Pats-Colts playoff game.
http://web.archive.org/web/20040215093250/http://msnbc.msn.com/id/4079437/
As for roughing the passer, I would like to see a link for your stats. From what I’ve seen, Brady seems to get favorable calls in big games.