First, bad teams ruin young QBs all the time. It isn't that they want to ruin the guy. They just do stupid things to ruin them like making a defensive coordinator the OC and a special teams coach the QB coach. I doubt Belichick did that to ruin Jones, but it was an unintended consequence.
Second, Brady had Weis (and **** Reibein in 2000) and Cassel had McDaniels to help develop them over multiple years.
Third, Zappe sucked last year. And you can make the argument that once teams got a book on him, he was as big as a disaster as Mac was when they benched him.
Fourth, I think you overrate how bad Mac sucked and how he was far worse than he could be because he turned into a head case in part because the Patriots set him up to fail.
Mac owns a majority of his failures, but he was set up to fail in New England. Not intentionally, but that was the results of Belichick's hubris.