Popularity contest. People voted for the outcome, Superman was not going to lose even if he was fighting GOD. Hell, Wolverine beat up Lobo with bone claws, Storm defeated Wonder Woman, Batman beat Captain America?? None of this is cannon in comics anyways, so basically it never happened.
This is the Professor Hulk who is a weaker version than the real deal Savage Hulk (or classic Hulk everyone grew up with) incarnation. And to make matters worst this Hulk at the time couldn't get stronger when mad because he would revert back into Bruce Banner. So he was at a major disadvantage to begin with.
BTW, the writer of the story couldn't mention this because he was told it would confuse the readers.
This comic proves nothing and I love Superman...