The World Tree, seemingly immutable, had not changed after centuries of sleep. The way it looked before slumber was identical to the way it appeared after awakening.
This was the cornerstone of all power in this world, the origin of Mana, the root from which gods were nurtured.
Aside from Elves, everyone's magic required chanting, or praising Mana, or extolling the gods. The power of magic originated from the gods, or in other words... for races other than Elves, the power of magic came from the gods' rotation of the World Tree's power.
Elves did not need this, Elves did not need to extol the gods... because gods, to a greater or lesser extent, originated from Elves or had intricate ties with Elves and the World Tree, rather than the other way around.
Therefore, the Church became the enemy of the Elves. The Church of the Unbelievers, the only church that denied the magic extolling the gods, denied the nobility of the World Tree, and denied the necessity of Elves' existence.