The overarching moral of the story is that individuals need to 'do their own thing' instead of blindly following the often restrictive rules and regulations of society. Jonathan feels held back by his family. They have certain, limited expectations of what a seagull is and how it should behave. But Jonathan can't accept such a stifling worldview. He wants to achieve perfection in flight, to soar as high in the sky as his talents will take him. That means defying his family and breaking the rules. Only by doing so can Jonathan achieve his dreams.
Jonathan provides an example of someone going against conventional wisdom and showing others what they're really capable of if they put their minds to it. There are countless examples in history of great artists, scientists, and innovators who challenged the accepted values of their society to achieve what had previously been thought impossible. And that's precisely what Jonathan does. His single-minded pursuit of excellence lights a path for others to follow, instilling in them the confidence that they too can achieve greatness and individual fulfillment.