At the traditional term tea for the Upper Middle class, Gene stands by and lets Phineas get away with outrageous behavior. Gene feels disappointed because he did.
After missing dinner one evening and being questioned upon their return by Mr. Prud'homme, Finny gives outrageous excuse after excuse and Mr. Prud'homme just laughs and doesn't take any action against them.
All through the novel, Gene lets Finny distract him from his studiies by getting him to jump out of the tree, go the beach, etc. Gene always goes along with him, even though it is against his nature. He doesn't stand up to Finny. Even when Gene tries to tell him the truth about the accident, Finny won't hear it. Gene never changes. He lets things happen when he could have stood up to Finny at any time. Finny "took over" Gene and Gene let him.