This touches on a question relating to epistemology, or how we gain knowledge.
The theist basically believes it is possible for humans to gain knowledge of God, either by evidence God exists through the senses and mind, or by God’s revelation by means of religious experience, miracles, scripture, and other means.
The atheist denies God exists so whatever ‘knowledge’ we have of God simply has an explanation in terms of either human belief or activity or cognition, or in terms of natural phenomena.
The agnostic denies that knowledge of God or any other transcendant entity or object is possible, usually because there is no conclusive evidence such a being exists or has revealed him/itself to us, or that our powers of cognition and understanding cannot know such a being or transcendant object.
This problem touches then on the question of human knowledge and of what human beings can and cannot know. The argument in the Matrix against the possibility of knowledge is basically that there is no way of telling which ‘reality’ which we experience in our minds is really true; it is possible (and in fact, it is true) in the Matrix that the ‘Matrix’ is a gigantic communal delusion of the human race made by their intelligent machine overlords. Yet to each perceiver in the Matrix, the Matrix is ‘real.’ Philosophers have formulated it another way; the brain in the vat paradox. Suppose some intelligent aliens, wanting to experiment on humans, came down in a UFO, abducted you, removed your brain from your body (ensuring it remained alive) and placed it in a special tank. The aliens, using their advanced technology, attach various information pathways to the nerves of various sense organs which simulate normal human experience on Earth. When the human being ‘wakes up’ (that is, the aliens turn the brain to a state of normal conciousness) how does the human know the reality is not a simulation, as it really is?
Descartes posed this problem himself in his Meditations, using ancient skeptical arguments, and instead of aliens assumed instead all sense impressions and experience were the work of a demon. He came to the conclusion that the only truth he could come to was that to exist and be aware of things, a concious entity must also exist necessarily. Descartes believed this was a rigorous proof that the mind and soul were immortal, even if the body perished, as when the existence of the body is shown to be a false belief by this skeptical method, the only thing left is conciousness.
Not all buy this argument and many reject it, or tried to present alternatives. One area of interest is how we can know which universe of experience is true, and which are simply illusions or delusions.
Descartes also offered a proof of God’s existence based on the reflections and method of doubt, on the basis that it was God who guaranteed that the external world existed and what Descartes believed to be true was true. He also argued from something called an innate idea, a sort of intelligible object the mind, abstracting from sense experience, contemplates and is led onwards to absolute and perfect Being (a similar path to the Absolute or God occurs in Plotinus and Augustine, and also in Indian contemplative meditations). Skeptical philosophers though argued Descartes was incoherent at many points and some believe the mind is basically the brain, and any ‘objects’ we encounter in cognition are either phenomena or appearances which don’t reflect a deeper underlying reality, or simply items of concious awareness our brain generates for us in our concious awareness.
George Berkely believed the last idea, and comes close to the Matrix when he argues all things are in fact simply ideas in minds, either human minds, angelic minds, or God’s mind. John Scotus Eriugena came to a similar conclusion in the early medieval period, though via a different route. This was rejected by empricists like Hume and also by Kant, though Edmund Husserl’s phenomenology in a way rediscovered this idea when he studied how the mind understands logical truths.
In terms of understanding God, it depends on whether one accepts cognition of the essence of God is possible by the human mind. Theologians seem to agree God’s essence is not something the human mind can grasp in its infinity, and the philosophers agree, though the human mind can still approach God by logical methods and contemplation to arrive at some statements about God which are true. St Thomas believed it was possible for the human mind to have cognition of God in the sense terms and concepts could be applied to God, but not in the sense the mind could grasp the divine essence (which requires the beatific vision).