Do you think maybe they booed it because they thought he was, you know, ATTACKING CHRIS BENOIT. You can't put over motive in commentary when the crowd at the show can't hear it. The fans did not know that he was going for the lone-wolf deal. The fans saw it as "He just FU'd Chris Benoit, BOOOO!"
If they didn't react at all...well, that's a whole 'nother story. But when one babyface attacks another babyface, it usually means that the attacker is turning heel unless it is already WELL established that the character is a tweener and will basically do what he wants. Cena wasn't being booked like that at the time, I do not believe.
Face Austin had DTA, Face Cena is more DOA.
Technically, by way of the booing, the angle DID GET OVER...sadly, it was not the angle Hayes was pushing for.