Make sure you understand the difference between a prefab and a game object that's been instantiated (cloned) from that prefab.
With the above code, it's unlikely that you're actually 'rotating a prefab'. If however that script is attached to the prefab, then any game object cloned from the prefab should indeed be rotated 90 degrees as soon as its Start() function runs.
Keep in mind though that Start() only runs once, sometime before Update() is called for the first time. As such, in this case it'd probably make more sense simply to instantiate the game object with the desired orientation (rather than modifying it after the fact in the Start() function).