The themes of Jonathan Livingston Seagull build on one another, culminating in the theme (message) that love and forgiveness are the all-important values in life. As Jonathan's mentor Chiang tells him,
Keep working on love.
But realizing the centrality of love comes only after Jonathan embarks on a long journey of self-discovery. This journey leads him, first, to understand he is different from the other gulls. They care about flying as a practical means to an end: for them, it is a tool to find food. Jonathan, in contrast, falls in love with flight as a thing itself. He spends all his time on the act of flying. He wants to soar ever higher and fly ever faster. He doesn't care if flying brings him food.
This non-conformity is not understood by the rest of the gull community, and the gifts of what he has learned are rejected by the other gulls. He is cast out. This angers him, though he is fortunate to be able to learn the knowledge of "perfect speed" by the gull Chiang in the higher realm he, Jonathan, has achieved.
All of Jonathan's wisdom and appreciation of flying is good, as is his arrival at a higher plane of existence, but—and this is key message of the book—the highest value lies in Jonathan's ability to forgive those who wronged him and give back to his society in love. Jonathan comes to understand this message and is able to go back to his flock as a loving and wise guide.