The Goober is Jerry's only friend. He's an ace runner. In fact, running even makes him smarter. We're told, "Even his thoughts became sharper, and things were simple and uncomplicated – he could solve math problems when he ran, or memorize football plays" (9.1).
He's a sensitive guy as well. After helping to destroy Room Nineteen as a Vigil's assignment, and seeing what it does to Brother Eugene, he feels extremely guilty. Likewise, he's very worried about Jerry, but doesn't know how to help him, other than to recommend Jerry accept the chocolates.
The Goober tries to show his support for Jerry by not selling any chocolates either, but his gesture is ignored; he's credited with selling some 23 boxes sold by The Vigils' sales team. Similarly, when he screams for Emile to stop beating Jerry at the raffle, nobody hears him. Although he doesn't save Jerry, he is there for him after the raffle, holding his head while they wait for the ambulance.