Headmaster Charleston expresses real doubt that Rory will be able to make it at Chilton, and lets her know that she won’t be offered any special help in the dog-eat-dog, sink-or-swim academic culture at Chilton.
Throughout the show Rory is depicted as not coping very well when anyone doubts her abilities. This time she remains calm, but by deflecting the situation in a passive-aggressive way, she also refuses to engage with the headmaster, or to argue her case with him and present herself as fully competent and up to the task (which is the response he is hoping to provoke). It’s the beginning of a worrying trend in Rory’s career.
The Annotated Gilmore Girls 