You can thank Kraft's original capitulation for the record never being set straight on this. Their surrender on this never sat right with me. But Kraft has made a ton of money with the Pats being cheating public enemy #1, so it's all good.
Kraft's capitulation? That's some seriously revisionist history. Kraft did't "capitulate," there simply wasn't anything he could do. Not only is there no formal process for a team to appeal a penalty, but under the owners' contracts with one another, they're not even supposed to publicly speak out against the commissioner's ruling.
Let's also remember that, while the significance of the infraction was blown out of proportion by several degrees of magnitude, the Patriots were technically guilty of what they were being punished for in that situation. What ended up screwing the Pats over during Spygate wasn't anything that Kraft did, but rather Belichick's refusal (despite Kraft's urging) to do any damage control w/ the media.
If, right out of the gate, Belichick had held a press conference in which he made clear exactly what the details of the infraction were (and, thus, how minor it was) and apologized for ignoring the memo, saying that while he may not have seen it as a big deal, he was neverthelesss wrong for not having deferred to the league's wishes on the matter, and that in the future, he would only record the opposing team's signals from league-approved locations.
Instead, by stone-walling and saying it was a league issue, and it was being handled by the league, and he had no further comments on it, he a) allowed the shouting heads of ESPN and the various butthurt ex-jocks who couldn't beat him during their playing days to set the frame for the controversy entirely unchallenged and b) came off as cagey and dismissive, making it seem like he had something to hide.
Now, we all know how Belichick feels about error-repeaters. That's why, this time around, he gave the (in)famous My Cousin Vinny press conference. But now, because of his unwillingness to do that kind of dog and pony show the first time around, the team already has a (undeserved) reputation, making it that much easier for Kensil et al. to set them up.