In The Matrix humans aren't really simulated. They have physical bodies and physical brains, but spend their life connected to VR machines. Usually those who hypothesize we are in a simulation mean the whole of our universe and the whole of us is running on some kind of computer and we don't exist in any physical sense in base reality. The Matrix doesn't need to raise currently unanswerable questions about human consciousness, since human minds are still embedded in physical meaty human brains.