To me, it looks like Brady liked his footballs a bit on the underinflated side (something that we've all known for awhile now), and made that desire known to the ball boys. Much like Aaron Rodgers, Brady had a preference that was well known. This most likely happened in a "Tom Brady-like" way where he *****ed and moaned about it, getting on them when the balls weren't right. As we know, Tom is a perfectionist, and does not allow anything to get in between him and winning.
Does this mean that he's a "cheater?" Hell, no--at least not to me, anyway. This means that the Pats' practices had no longer become a secret, and that all it would take is a whining team like Irsay and the Colts to bring this to the attention of the league. Unfortunately, in the era of Commissioner Goodell, this had "bad news" written all over it from day one. As noted, had this been Tagliabue or Rozelle, we'd never have heard about this minor issue.
The kicker is this = it probably really didn't give him that much of an advantage, if any, other than the right kind of feel in his hand. Now once again, reputation and punishment comes into play. It's a terrible shame.