Why does Jem cry at the end of chapter 7? What does Jem understand about Boo and Mr. Radley that he didn't get before?

Jem and Scout walk past the Radley property each day on their way to school. Inside a knot-hole in a tree on the property, they discover little gifts such as chewing gum, a ball of twine, dolls carved from soap, a medal, and a pocket watch. One day, Jem decides to write a note to thank the person that has been leaving the gifts. As he approaches the tree to leave the note, he notices that the hole has been filled with cement.
The next day, Jem sees Mr. Radley and asks him if he filled the knot-hole in the tree. Confirming that he did fill the hole, Mr. Radley explains, "You plug 'em with cement when they're sick." When he questions Atticus about the tree, and Atticus says he believes the tree is healthy, Jem realizes why Mr. Radley filled the knot-hole.
Scout and Jem believe that it is Boo who has been providing the gifts in the knot-hole of the tree. In filling the hole, Mr. Radley has put an end to the only connection the children have ever had with Boo. Realizing that Jem is upset, Scout leaves him alone on the porch. When Jem enters the house, Scout, "saw he had been crying; his face was dirty in the right places." Jem is probably upset about Mr. Radley filling the hole because he realizes how alone Boo must feel. Boo's attempts at reaching out to the children have been put to an end.