In this video from 2006, Richard Dawkins provides an evolutionary explanation for why our intuitive understanding of the world is limited. Our brains have evolved to help our bodies find our way around the world we perceive: "We never evolved to navigate in the world of atoms... we operate in a middle world — perceiving a reality somewhere between the atomic world and the cosmic world." ..."What we see of the real world is not the unvarnished real world but a model of the real world, regulated and adjusted by sense data—a model that is constructed so that it is useful for dealing with the real world. The nature of that model depends on the kind of animal we are."
What I take from this is that we must become a bit more skeptic about the validity of our own intuitions, accept our own ignorance more and embrace science more. Through science and technology we can increase our capability to perceive and measure the very small and large and we can test our intuitions in carefully designed experiments. In doing so we can develop our knowledge about the unvarnished reality and improve the human condition.
Also read: Objective reality as an asymptote