Our brains have evolved to deal with issues at our own scales: mates, rivers, apples, rabbits, and so on. Our brains simply weren't built to understand the fabric of reality at the very small scales (quantum mechnics) or the very large (the cosmos). As Blaise Pascal put it, “Man is equally incapable of seeing the nothingness from which he emerges and the infinity in which he is engulfed.”
~David Eagleman via Boing Boig
I'll add a short caveat to Pascal's observation about our lack of ability to see the quantum void of raw potential or the scope of the universe on the cosmological scale. We are equally incapable of seeing these realities, at this time.
The brains we have today are the augmented apparatuses that our children and their descendants will have tomorrow. Even as we learn about how the minds our brains generate are limited by the constraints of biology and our evolutionary history, we are developing the knowledge base and the technologies to push back the organic boundaries that constrain our comprehension.
Not that I'm working on publishing a military science fiction novel about this or anything...