Jem was suddenly forced to recognize that not everything in life is fair and not everything works out the way we expect it to. He had spent his entire life believing that the people in his community were, overall, pretty decent people. When the jury found Tom Robinson guilty, it was like a caterpillar being forced out of its warm, safe cocoon into the harsh light of day - the cold, real world. Jem never believed the jury would find Tom guilty - he believed Atticus could convince them to see the truth. What he did not realize until the verdict came in is that even knowing the truth, which the jury probably did, they still were not going to side with a black man against a white woman.
Jem has had an ideal model of innocence he tends to refer to constantly: that though obstacles may be present (Bob Ewell), the innocent and good will eventually prevail (Tom Robinson). When Tom Robinson was declared guilty by the jury, Jem's ideas of innocence were immediately crushed by the unrelenting cruelties of racial prejudice which continue to influence the actions of Maycomb even during the trial. By coming out of his cocoon, Jem must face the cruelties of reality and abandon the shielded environment Atticus has created for him. As the ideal model of justice, Atticus has continued to impose his own righteous morals and values on Scout and Jem which has influenced their views as well on racial prejudice/stereotyping.