Then, if Naughty Dog chooses to ignore the author's claims of copyright infringement, he could make a big stink over it. Personally, if I was the author, I'd be honored to be in a game of that magnitude at all. In other words, it should be a good selling point for the author from now on.
"Oh yea, you know that best selling, perfect game, The Last of Us? Yea, they used some of my art in there... Oh yea, no big deal."
Truthfully, if they had contacted the author before incorporating it into the game, and they found out it would cost money, they probably would have found another map, or make one of their own. A company that large has the man power to make a subway map.
I won't argue that the author has a right to be upset, but don't just start some type of flame war against a company that people love right now.