I can only answer one of the two questions presented, so I will address whether or not the quote provided is a theme of the story.
Knowing Bradbury's work as I do, I cannot imagine that he would ever suggest that any knowledge should be suppressed. I believe that he would expect people to be exposed to all knowledge and be allowed to decide for themselves how best to use it. (This is a theme in Bradbury's novel Fahrenheit 451.)
Knowledge comes with responsibility. Bradbury seems to recognize this, but also believes that people should be given free will to make their own decisions, and learn by their mistakes if necessary.
I don't believe that the theme of "The Flying Machine" is that "...certain knowledge should be suppressed for the good of the majority." No one should police one's thoughts or beliefs. If this were ever the case, who would "police" the police? I believe that Bradbury portrays the Emperor as a leader with limited vision and unrealistic expectations of his ability to control the world around him. I do not believe that Bradbury supports the Emperor's actions or philosophy, as it is stated in the quotation above.