JESS: Oh, come on, let me see your withering stare.
RORY: It’s dangerous. I could hurt you.
JESS: I’ve been hurt before.
A serious statement masquerading as a joke. Jess truly has been hurt by life, and he’s probably also been hurt by Rory, and her efforts to keep him at bay and continue seeing Dean, even as it became increasingly clear that she didn’t really want him any more. Jess comes this close to saying, “You’ve hurt me before”. Don’t worry Jess – Rory has more emotional pain in store for you!
Note that Jess and Rory walk past a florist’s, a romantic symbol, but it’s selling balloons – condoms can also be used as balloons. The car driving past has a licence plate of INQ 069 – ink + 69, as if writing and sexual attraction is what’s drawing Rory and Jess together. Sex, romance, reading; the holy trinity of Rory and Jess!
(This is the second licence plate ending with 69 I’ve noticed, so it might be a running joke, although last time it could have been highlighting the sexual attraction between Lorelai and Christopher).
The Annotated Gilmore Girls 