This is not an insight that Jonathan arrives at by himself. The words are spoken by Jonathan's instructor, Sullivan, after Jonathan had reached what he believed to be heaven and was able to practice his flying with other seagulls who had the same dreams and aspirations as he.
Sullivan tells Jonathan 'You are pretty well a one in a million bird', to make Jonathan realise how special he truly is. Instead of following the trend and being 'normal', as other members of his flock, Jonathan had decided to achieve perfection in flight. His different attitude lead to his banishment from the flock and he became an outcast.
Other seagulls in Jonathan's flock subscribed to the basic norms of their society, flying for food, fighting and not being desirous of achieving anything much, but existing and meeting their most basic needs.
What makes Jonathan exceptional is that he does not give up, he tenaciously seeks to learn more, taking risks in the process and discovering more about himself, life and purpose. Jonathan finally learns from Chiang that heaven does not exist but that heaven is perfection, which is not defined by any physical space or time, but is a place which exists in the mind.
A remarkable tale of inspiration and affirmation!