In John Knowles coming of age story, "A Separate Peace," several major events impacted Gene during his time there. Two of these events took place at the tree and the marble stairs.
The simple answer to your question is that Gene fears seeing the tree and the marble stairs because this is where Finny was injured and eventually caused his death. Each incident took a part of Finny away from Gene and destroyed their easy camaraderie.
Gene fears returing to these areas of Devon School after fifteen years, because these two places are where he committed his "crime" against Finny. He feels drawn to these places because he must find some "Separate Peace" from the terrible thing that he did to Finny. He returns to come to terms with his actions during those few years in his life that helped to create the man he now was.
"Finny looked steadily at me, his face very handsome and expressionless. "What do you mean, you caused it," his voice was as steady as his eyes.
My own voice sounded quiet and foreign "I jounced the limb. I caused it." One more sentence. "I deliberately jounced the limb so you would fall off."
He looked older than I had ever seen him "Of course you didn't."
"Yes I did. I did!"
"Of course you didn't do it Youdamnfool Sitdown, you damn fool."
"Of course I did!"
"I'm going to hit you if you don't sit down."
"Hit me!" I looked at him. "Hit me!" You can't even get up! You can't even come near me!"
As you continue to read the story, it will be revealed that these two places are where incredibly significant and awful things happened to Finny, Gene's best friend back in his school days. The tree is where Gene caused Finny to fall and break his leg the first time, and the stairs are where Finny fell the second time after realizing that Gene had hurt him the first time. Both of these places led to Finny's surprising and awful death, and going back to look at them brings all of these memories back for Gene.
These memories are fearful because they reveal just how selfish and petty Gene was back in those days; it was his own insecurity that led to Finny's demise, and facing that is a scary thing. Imagine having to face the fact that you are partly responsible for your best friend's death. That is super hard to do, and scary, because it forces you to admit that you are a pretty weak person that is capable of harm and evil. That is why those places are scary for Gene--they remind him of his own dark side, and the death of his very best friend. He wants to see them because they are a vital and crucial part of his own personal history, and he is ready to face down those demons and process what has happened.
I hope that helped; good luck!