It hurts. It hurts to know that her safety is going to leave him alone and friendless in this hellhole, and Hermione wants to go to him and try to comfort him...only she knows her attempt wouldn't be welcomed. There are some things that Malfoy doesn't want her to see, and wouldn't thank her for intruding upon. And besides, there is nothing Hermione can say to make it any better. Unless she stays, or he goes. And the idea of staying is unthinkable to her – much as the idea of leaving seems to be to him.