What is the moral of the song?

Often we try to do something as a gesture of good will and it is interpreted as a declaration of war. People are so conditioned to assume "those ones over the wall" are trying to destroy them that they will look for any provocation to justify their blind hatred.

As a result, the world will torch itself before considering that the intent of 99 red balloons going by was just meant to lift people's spirits up, if only for a moment.

(This song is mostly written with the context of the Berlin Wall and the tensions of the Cold War).