The standard answer is that all of our naive beliefs about the world would be false. You are not actually sitting on a couch, your simulated body-projection is simulated to be sitting on a simulated couch. The very fact we can't tell whether or not we're in the matrix undermines all our knowledge.
The more insightful answer is that even if we're in the matrix, everything about the physical world is still true, there is just a metaphysical fact we are unaware of--namely, that the universe happens to be a simulation. You're still sitting on a couch, and the couch is still made of atoms, and the atoms are still made of subatomic particles and so forth, but it turns out all the subatomic particles are just data structures in the matrix and we didn't know that before. Nothing is undermined.
You could even argue that metaphysical statements are meaningless, though you run into problems going too far that way as well.