Because it can convey its meaning without a direct object, the verb "fly" is intransitive. Without describing the plane's flight path, the flying activity is finished. Although it is not the direct object of the verb, the preposition "over the mountain" adds more information about the flight's path or direction.
A transitive verb, on the other hand, needs a direct object to fully express its meaning. For instance, the verb "fly" is transitive in the statement "The pilot flew the plane" since it needs the direct object "the plane" in order to make sense.