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 blackest day, in brightest night, beware your fears made into light. Let those who try to stop what's right, burn like my power: Sinestro's might!"