A group of rocks floating in the air - anyone from Earth visiting Gaea, like Hitomi, could not help being overwhelmed at such a sight. However, these rocks have always existed in Gaea ever since it came into being. The people of Gaea, including Van, have never regarded these stones as anything special. Of course, it was natural for the people of Gaea to try to develop a means of transportation utilizing these special rocks.
However, in the early stages of Gaean civilization, these attempts ended in vain. Even though they knew that heating the rocks increases floatation, people still could not effectively deliver the amount of heat needed, and they were unable to skillfully navigate these ships. To overcome these difficulties, early transportation using the levitation rocks - floating ships - utilized sails for propulsion and were anchored at destinations with ropes.
The situation changed dramatically when a system using the energist - their equivalent of our internal combustion system - was invented. Both a heat source and a propulsion device were obtained at the same time. (However, ships like the Crusade still relied on wind for additional propulsion.) As a result of incorporating the energist, floating ships became more expensive. And since ocean ships were a more affordable means of mass-transportation, only royalty and the rich owned floating ships. Still, development of floating ships had an immeasurable influence on later progress of the civilizations of Gaea. After all, it is a well-known fact that advances in communications and advances in civilization are heavily related.
One final addendum: Zaibach Guymelefs are also powered by levitation rocks, which is what enables them to fly.