Re: "The Dark Knight Rises" Review and Discussion Thread (spoilers)
Gordon could have very easily put it all together if he wanted to. That's the thing, though. Gordon doesn't want to. He explicitly states that he doesn't care who Batman is. That's always the way it's been in the comics, too. Gordon doesn't know because he doesn't want to know. Once, when Batman offered to reveal his identity, Gordon told Batman that if he wanted to know, he already would.
"In Brightest Day, in Blackest Night, no evil shall escape my sight. Let those who worship evil's might, beware my power: Green Lantern's light!"