The Clouds are pretty important to the action, so it seems only right that they get to be in the title, right? They're godlike entities that, represented by the Chorus, get to weigh in on the play's events and deliver their opinions and moral judgments to the characters (and the audience).
Of course, on a more symbolic level (see "Symbolism, Imagery, Allegory"), they represent the kind of fluffy intangibleness of the thought that Socrates is pushing on his students. Real clouds are just insubstantial vapor, and so (the play suggests) are Socrates's ideas. With references to the clouds firing on that many cylinders, we can't imagine naming the play after anything or anyone else.