"Any fear I had ever had of the tree was nothing beside this. It wasn't my neck, but my understanding which was menaced. He had never been jealous of me for a second. Now I knew that there never was and never could have been any rivalry between us. I was not of the same quality as he."
Gene says this quote, and it reveals what he really fears about Finny. He doesn't fear Finny's athleticism and lovable character. Gene fears Finny's goodness. Finny is truly an altruistic character in the novel. He is basically incapable of thinking wrongly about his friends. He can't imagine not wanting what is absolutely best for his friends. Gene simply cannot relate.
"What did he mean by telling me a story like that! I didn't want to hear any more of it. Not now or ever. I didn't care because it had nothing to do with me. And I didn't want to hear any more of it. Ever."
This time Gene is afraid of what Leper told him. Not because Leper threatened Gene, but because what Leper described was exactly what was happening to Gene.
"Preserved along with it, like stale air in an unopened room, was the well known fear which had surrounded and filled those days, so much of it that I hadn't even known it was there. Because, unfamiliar with the absence of fear and what that was like, I had not been able to identify its presence."
This quote came early in the novel (chapter 1). Gene is describing the feeling of fear that had surrounded him during the events of the novel and his time at the school. Gene admits that at the time he didn't know it was fear though because it was the main sensation he experienced. It sounds weird that he wouldn't know fear unless he could compare it to not being afraid. But it does make sense. Would you know true happiness if you never had experienced sadness?