When Nathan Radley fills the tree knothole, it distances Boo from Scout and Jem.
Boo Radley is not a normal person. He is very reclusive, and never even comes out of his house. Scout, Jem, and Dill begin to bring him out of his shell with their efforts to contact him. He strikes up a friendship with them through the simple means of leaving presents in the knothole of his tree.
The children do not know who the gifts are from at first, but Boo keeps leaving them. The little trinkets are his way of connecting with them. He gives them gum, pennies, twine, and even a watch. The best present and the most personal is the soap dolls. They are perfect miniatures of Scout and Jem.
Nathan Radley, Boo’s older brother, is almost as quiet as Boo. However, he does not seem to want Boo to interact with the neighborhood kids. Maybe he feels it is inappropriate. Nathan tells Scout and Jem that the tree was sick.
“Mr. Radley, ah—did you put cement in that hole in that tree down yonder?”
“Yes,” he said. “I filled it up.”
“Why’d you do it, sir?”
“Tree’s dying. You plug ‘em with cement when they’re sick. You ought to know that, Jem.” (Ch. 7)
The children ask Atticus if the tree is sick and he doesn’t think it is. Jem in particular feels very badly about this. He knows that Boo Radley meant no harm, and that now he has no connection to the outside world. When Boo leaves a blanket on Scout’s shoulders, Jem insists that Atticus not return it. He doesn’t want Nathan to know that Boo was there.
“…Mr. Nathan put cement in that tree, Atticus, an‘ he did it to stop us findin’ things—he’s crazy, I reckon, like they say, but Atticus, I swear to God he ain’t ever harmed us, he ain’t ever hurt us, he coulda cut my throat from ear to ear that night but he tried to mend my pants instead… he ain’t ever hurt us, Atticus—” (Ch. 8)
Jem and Atticus both understand that Boo needs his connection to the kids. He has no one else. Cementing the tree was cruel, in Jem’s mind, because Boo did nothing wrong. He thinks Boo is harmless, but Nathan must not have thought so. Still, cementing the hole made poor Boo even lonelier.