Incorrect perception is a theme within the play which is illustrated by the storm.
The destruction of the Turks lulls the characters into a false sense of security: the enemy is dead, therefore they can rejoice and celebrate. However, the Turks are not the real enemy - it is Iago and his evil machinations. The idea of judging by appearance, as happens with Othello, himself, is revealed to be flawed. Iago is trusted by many, not just Othello. Desdemona is revealed to be more wilful than her father anticiated, and Emilia puts her mistress before her husband when integrity demands so.
The literal, external storm that destroys the Turkish fleet seems to promise peace, safety, and happiness for most of the people on Cyprus. However, it is the figurative, symbolic storm inside of Iago that leads to tragedy for many different characters. Like the external storm, Iago is an agent of chaos and disorder. The external storm destroys the pagan Turks; the storm personified by Iago destroys many of the play's most admirable Christians. The external storm destroys the ambitions and reputation of the Turks as great military figures; the chaotic storm personified by Iago does much the same to Othello.