When Miramax first started looking for directors to take on Good Will Hunting, they considered working with heavy-hitters like Mel Gibson, Steven Soderbergh, and Michael Mann. Affleck and Damon also asked their good buddy Kevin Smith if he was interested, but he responded by saying they actually needed a "good director" to do this movie. (Say what you will about Kevin Smith, but he has perfected the art of self-deprecation.)
So eventually, Damon and Affleck decided to go with Gus Van Sant. And it's not like they had to settle for anything less with this guy, who would go on to direct other award-winning films like Finding Forrester (2000), Elephant (2003), and Milk (2008).
P.S. Hey, Jay and Silent Bob fans. There's a joke in the movie Jay and Silent Bob Strike Back about how director Gus Van Sant "sold out" after Good Will Hunting. Here's the scene. Check out Van Sant literally counting his money behind the camera.