Ive never watched short animation created by Tezuka Osamu, and the Mermaid, was really unclear.
But I will show my own interpretation of this story.
I think this story is kind of a criticism of some countries which suppress peoples' freedom of having any kinds of thoughts. This Animation came out in 1963, and in that age, there might be many countries like that. Osamu might had known the fact that a nation's suppression on peoples' thoughts destroyed their imagination.
so, when the boy finds a fish becoming a mermaid, and took her to a town, the boy was arrested by guys who looks like police. Through the reformation of the boy's thoughts by those police, the boy becomes unable to see the mermaid. this indicates the destruction of the boy's imagination.
In the end of this story, the boy goes into sea with mermaid, which represents the boy's free imagination, but I think this scene indicates the boy's death. He chooses his imagination, instead of his life. from this scene, I think we can see an Osamu's special wish to people to have free imagination.