Windstones are magical minerals formed of compressed magical energy, energy similar to that of elves' 'Magic of the Firstborn'. Other similar minerals are the Firestones minerals aligned to the element fire instead of air.
Windstones can be created by the land gathering magical reserves and turns it into a crystallized form slowly, or artificially created by elves by compressing magical wind energy.
The humans of Halkeginia can mine these minerals which are close to the surface, but deeper reserves can only be acquired by elven techniques of mining. In Halkeginia, humans use these as a power source for the airships. The Jomungandrs golems created by the Mind of God also uses these as a energy source.
Windstones and its threat to Halkeginia
Later in the novels it is revealed the reserves of Windstones under Halkeginia has grown to the point where the continent will be ripped apart as the Windstones reach critical mass and start to float out of the earth, dragging the surface of the continent with it. Eventually the Windstones would dry out once in the air, and the floating land would drop down back to the surface. The last time such an event happened the island of Albion was formed, and there is the possibility Albion would fall back to the surface eventually.
Over 50% of Halkeginia would become uninhabitable once the Windstones start to rise, and due to the loss of resources as the surface breaks apart, humans would war between themselves for what little is left, and will lead to their extinction.
The Pope, Vittorio, claims that conquering the Holy Land is the only way to avoid this fate. There is enough resource there to satisfy everyone and they can migrate there to avoid the desperate war when people fight one another for resources, and that the Founder left a device there to prevent the Windstones from destroying Halkeginia.
Needless to say, both those points are deceptions. What the Holy Land holds is a vital component for Brimir's spell that commits genocide on other races, and Vittorio plans to eliminate the elves so humans can take the resources of the elves and provide a safe haven while Halkeginia falls apart.