Arceus is a god of creation not meant to intervene directly in the world's affairs, so when Groudon and Kyogre's feud threatened to tear the world apart, it created Rayquaza as a peacemaker. Yet as tension turns moderation to extremism, and war leads in turn to more war, so has Rayquaza's cult never been able to match Kyogre or Groudon's and inspire men to create a world of peace and harmony. For even if Rayquaza were not a god of peace, the sky does not offer Man the bounty of the sea or land, only a target for his dreams.
There have been places in Hoenn where Rayquaza did inspire devotion; the builders of the Sky Pillar paid this god homage, as do the people of Fortree City today, who live in treehouses and train birds and dragons. But far from mediating conflicts, Rayquaza's followers, with the notable exception of Oda Nobunaga, have been forced to withdraw from them to preserve their own lives.
It is only with the fears of the modern era – new wars with far deadlier weapons than old and the folly of civilization endangering the planet's very ecosystem - that Rayquaza has begun to earn Man's prayers. When chemical usage by humans began to deplete the ozone layer, Rayquaza became a symbol of the fight to protect first its ozone habitat, and then the environment at large. And in an age where environmental damage is joined by Team Aqua and Magma's efforts to summon forth the warring titans of old, many have found comfort in the idea of a god trying to keep everything in harmony – and inspiration, too, for Rayquaza can not triumph alone.