What comments of his did you find “out of line?”
As for his other comments -- well, it was McCain's event, after all, and he gets to set the tone. And thus he has the right to object when somebody purporting to speak for him tries to inject a harsher tone than McCain wants to use.
And, fwiw, I think McCain's got a better bead on the mood of the electorate than Cunningham does. Cunningham is a professional loudmouth, who was doing his normal schtick ... but I strongly suspect that the typical talk-radio innuendo attack won't work against Obama. It will cause the middle-ground voters, who are already somewhat attracted by Obama's charisma, to feel like defending him -- to McCain's (and our) detriment.
As to the issues he raised, especially Rezko .... are they legitimate? Sure they are. But if they're going to become campaign issues, they've got to be approached in the right way. You'd have thought the Clinton years would have taught Cunningham a thing or two about that. Apparently not.