At the heart of the Enlightenment is an attempt to reconceptualize perception and give it a solid and universal foundation. There is a question of what it is that we know, how we know it, and what the limits of that knowledge might be that begins with Locke and reaches its outer limits with Kant. This project aims at developing knowledge of the world that is individual and empirical through a method that is universally applicable. It also stems from an common belief amongst Enlightenment thinkers that individuals must cease to be beholden to inherited ideas, an idea that recieves its most characteristic expression in Kant's "Have courage to use your own understanding!"
Locke's Essay Concerning Human Understanding is important as one of the first attempts since Aristotle (see also: Francis Bacon) to describe human perception. Locke's major contention throughout the essay is that there are no innate ideas: everything that we understand comes to the mind through passive Perception and Reflection, and then may be elaborated through the active mental processes of Combining ideas or Abstraction. However, the mind is an empty curio drawer upon birth and every idea we have ultimately originates in passive perception of the world around us. William Blake opposed Locke because he felt that this understanding of perception destroyed the power of imagination, but one needn't be an artist to find Locke's tabula rasa a bit depressing.
Locke's Essay is revolutionary because it puts human knowledge on a universal foundation. Locke doesn't tell the reader how to think; just that he should trust the knowledge that he gains by his own perceptions. There is an implied challenge to religious scripture here, but Locke does not follow through with it, instead arguing that our perceptions offer us knowledge of the existence of God based on the a priori argument- if everything we percieve had its origin in another thing, ultimately there must be a first cause of all being and power which is logically God. However, I think that Locke's empiricism makes it difficult to accept the accounts of miracles in the scriptures. David Hume, in his Lockean Enquiry Concerning Human Understanding, actually develops the argument that accounts of miracles in the scriptures cannot be established based on eyewitness testimony of events that go against the laws of nature. Hume's skepticism of miraculous accounts would seem to discredit key scriptures such as the miracles performed by Moses, or even the resurrection of Christ.
However, Locke does not go quite so far, arguing that knowledge of God can be gained through the senses, and counciling only against religious conflict. In his Letter on Toleration, Locke makes the point that the limited nature of our own brains makes it impossible for any of us to believe that we have the sole truth about something as mysterious and speculative as the nature of God. In a sense, Locke could be seen as arguing for humility in regards to things of faith, and not atheism.