When Gene speaks to the doctor following the surgery, the doctor tells him that Finny's leg had sustained "a messy break," and that although he will walk again, he will never be able to play sports as he used to. Gene reacts by bursting into tears, crying
"...for Phineas and for (him)self and for this doctor who believed in facing things. Most of all (Gene) cried because of kindness, which (he) had not expected."
Phineas had been naturally gifted with a flowing athleticism; sports had been as much a part of his life as breathing. Gene knows that to suddenly be rendered incapable of participating in sports would be especially devastating to Finny. He cries for Phineas because of the magnitude of his loss.
Gene cries for himself because of his complicity in causing the accident that has maimed Finny. Finny looks at Gene as his best friend, and in a moment of confused and hidden resentment, Gene has betrayed that friendship and inflicted a serious injury on one who has no ill-will towards him, and values him the most.
Dr. Stanpole is a skilled and sensitive man who sees a lot of pain and suffering, but he is practical, and insists on looking at things realistically and making the best of bad situations. I believe Gene cries for the doctor because his stoic acceptance of the destruction he sees everyday has a certain poignancy. He is a man of feeling who faces life head-on and takes things as they come. Somewhere deep within himself, Gene understands that, because of the war, Finny's injury is only the beginning of the pain and suffering the doctor will have to witness, and accept with a stiff upper lip.
Gene cries because of the unexpected kindness with which the doctor speaks to him. Because of the knowledge of his own guilt, he does not feel that he deserves it. In addition, when a person is trying to control huge and heartfelt emotions, kindness has a tendency to penetrate his defenses and cause him to lose that control, allowing feelings to burst forth in an avalanche of tears (Chapter 5).