»How does Link know who superman is?«

Link (about neo flying): "He's doing his Superman thing."

How does Link know who Superman is?
He was never in the Matrix

Superman is/was a considerable pop-culture icon at the end of the 90s/beginning of the 2000s, which is what the current Matrix is, in terms of timeline. As the Architect hinted, the Matrix is based off of human history; many of the escaped Zionists undoubtedly recalled such pop culture and passed it on to ZIon as a whole. Thus I do not think it's much of a stretch for Link to know who Superman is.

Superman is one of the oldest superheroes and is part of human society for more than 50 (80?) years now.

I think this question is out of the order...

Why should Link know Superman?
As an operator, he's watching the Matrixcode for long times. Somebody in the code could have been watching Superman some time. And he picked it up.
Something like that...

If you wonder why he knows Superman,
You could also start wondering how they got all the update-programs (learning kung-fu, karate, flying a helicopter)... because I also haven't seen them doing that inside the real world.

they probably take the information they need from the matrix, like a 'flight manual'; Bruce Lee's fighting style, books, movies, music into their construct program and convert the files so that they can be downloaded into yer brain, or be read as script

maybe Link reads a pdf file of Superman comics

there probably is no printing press in zion and they use computers a whole lot, like we do today, who is to say that Link cannot read Baudrillard or anything else while sitting at home at his computer

The operators also use familiar expressions. Tank: Hey Mikey, I think he likes it! I have often wondered how the natural born operators can read the code without ever seeing the things they represent. How would Link now the dangers of "incoming fire" from the twins when he should have no concept of a gun, except the thing that Dozer was killed with. I think that maybe that when they hack into matrix they can go beyond and hack into computers. I think maybe they have found a way to link up with the net, maybe through the construct. Maybe they found a way to decode certains parts of the matrix (like the net) just not all of it into discernable images and text.

BUT, remember what morpheus said. "Nobody can be told what the matrix is...."