Why would anyone choose the map rather than the territory as their foundation? Why engage in science if you are not willing to accept the inferences that it makes about reality? Am I not going to believe in atoms because it doesn't match what I see with my eyes? If there is no evidence of the physical world then why don't you walk through walls? Do you have any explanations of illusions? Talk about making a mockery of rationality!

The parent post may have been exaggerating a bit; in any case, its basic point is right. We have to start with the map; we don't have direct access to the territory. We believe in physical reality and atoms because they seem to explain our experiences well. It's not naive realism or idealism to point this out.