The Church opposed many of the new ideas of Enlightenment because the people were beginning to think for themselves, and weren't as willing to accept things just because the Church said it was right.
Enlightenment encouraged people to rethink the rights of absolutism and mercantilism.
The thinkers of the Enlightenment could not find any scientific proof that the Monarchs were any better than regular people, and the Church didn't agree, as monarch were 'chosen by God'.