I think this is an instance where we have to keep two conflicting ideas in our heads at the same time.
Yes, Bob Kraft breathed life into a moribund Franchise that was trying to move out of town and he deserves full credit for his gut instinct that BB was worth a first rounder and yes he deserves full credit when he didn't interfere (a la Dan Snyder) when Belichick went with Brady over his own favorite (at the time) Bledsoe...all of those things...and much, much more...are true.
But he completely blew his handling of the Deflategate nonsense from San Francisco on. He should have been angry and defiant over the League's behavior instead of "making nice."
He's too smart a businessman to have thought that being "nice" was going to make any difference in how Goodell and the owners would (mis)behave. The latter was not only naive but arguably disingenuous. He has since repented of that mistake, but the damage was done. He put, at the time, his "feel good" standing in the club of owners over his Quarterback and his organization and his fans.
The good he has done outweighs that error, IMO, but it was a very big error by a man who has also done a lot of good.