I disagree with his politics as well, and he was an uneducated man, so I think there is a good reason for his bad decisions.
It is easier to lead an uneducated person down wrong paths, especially when they get lots of attention from being famous.
I give him credit for going to jail instead of running to Canada.
I also give him credit to almost immediately in the days following 9-11 to come out and denounce this not as a religious act of a faith, but as a criminal act of terror.
Even you have to say, with the little that all other Muslims have said against Islamic terrorists, Ali was impressive compared to the rest of the world leaders of that cult.
By the way, you can almost bet the farm that Orrin Hatch who persuaded Bush to make this award to Muhammad Ali. Hatch loves celebrities, and Ali has been one his faves for decades.