The injury had something to do with it I'm sure but that's not to say that Hughes wasn't going to win that fight be either decision or stoppage in the 3rd round or later.
Penn is a very good fighter but conditioning is not his strong point. If he can't put the guy away early, you have to give the advantage to the other fighter. As for not having the drive, I think he showed that when he won the belt the first time and then just walked away from the company.
You still have to believe that Penn and Hughes will fight again in a rubber match.