The central message of the book is that everyone is a valuable member of society, and everyone can contribute to the common good. In Messenger, we learn about Village, an altruistic community where everyone who seeks refuge is accepted. Indeed, people come from all kinds of regions run by oppressive governments, but soon they are able to shed their past, and with the help of the villagers they are integrated into their community.
All of the villagers, although not the most perfect looking, have good hearts and use their best quality, as indicated by their true names, to help others. The schoolteacher, for example, is called Mentor, as he is much more than just a teacher; to Matty, he is almost like a father.
Finding one's best quality takes time, however. Matty dreams of being called Messenger, thinking that he is best at delivering messages through the hostile forest. However, it turns out that he has an even greater gift: The ability to heal--which is why in the end Leader names him Healer.
As soon as the villagers focus on their outer, superficial appearance and start keeping secrets, they lose their good personalities. Even Matty speaks condescendingly about Kira, who has a crooked leg, and he wonders how Leader can call her 'lovely.' However, when he tries to convince her that her leg should be healed and she refuses, he learns that impurities are part of one's identity and something to be cherished. Losing the impurity would mean losing one's identity, as Kira points out.
For teenagers going through puberty, these are powerful messages indeed: Learn to be proud of yourself, discover your gift and best quality, use it help others, be honest, trust that you will find your place in society, and put the common good above your own.