Even though Goober empathizes with Jerry, why doesn't he do anything to intervene?
This really is one of the central problems of the book -- the inability of people to go against the prevailing will of the herd, even if the herd is unjust. Goober, who is a good kid, really, was not possessed of Jerry's moral courage. Jerry was the kind of person who was able to stand up to evil in his environment (personified by the Vigils, particularly Archie Costello). If you recall, Jerry didn't even particularly want to stand up to the Vigils (by refusing to sell chocolates and, finally, taking part in the horrible "assignment") but he felt he had to resist. He wanted no one -- not even his own father -- to help him in standing up to Archie and his "goons".
Goober had none of these feelings, but he did experience fear and the desire to get away from Trinity and the Vigils. Goober's fear is represented by Cormier as the kind of feeling most people have when faced by an unjust majority -- while Jerry is shown as an individual who is rare. Jerry's kind of moral courage is not found in most people, and Goober recognized that and couldn't understand Jerry. If Goober had, possibly, a friend who agreed with him he might have covertly tried to help Jerry, but Goober alone was unable to face the wrath of the mob.