You thought a Red Sox game as a metaphor for love was weird? Try this one on for size: Farting, at least in the world of Good Will Hunting, is an even bigger metaphor for l'amour.
Will seems to think that if he stays with Skylar, it will ruin his experience of her because he'll find out all the ways that she isn't perfect. But as Maguire tries to tell him, it's people's imperfections that tend to make us love them:
MAGUIRE: You know what? [Nancy] used to fart in her sleep. Sorry I shared that with you. One night it was so loud it woke the dog up.
At first, Will thinks they're just having a laugh, but Maguire sums up his point in saying,
MAGUIRE: People call these things imperfections, but they're not, aw that's the good stuff. And then we get to choose who we let in to our weird little worlds.
Part of Maguire's therapy is teaching Will to let go of his fears and hang-ups so he can go out and experience life, even if a lot of stuff might be scary. There's no question that Will is afraid of getting emotionally hurt. But as Maguire tells him,
MAGUIRE: Now you can know everything in the world, sport, but the only way you're findin' out that one is by givin' it a shot.
By "that one," Maguire is referring to the happiness of knowing all a person's imperfections and still loving them. And by the end of the movie, it looks like Will has taken a step toward learning this by heading to see his girlfriend Skylar in California.