[Rory exits the diner and runs to catch her bus as Luke walks over to the table]
LUKE: Fast runner.
DEAN: It’s the coffee.
LUKE: Not your face?
Luke is very resentful of Dean for standing in the way of Jess being with Rory, which is what Luke wants for him. (That may suggest he’s not as thrilled about Jess being with Shane). Here he gets a dig into Dean, implying that Rory should be running away from him. I don’t think he ever really forgave Dean for breaking up with Rory early in their relationship.