There is a big difference between how we perceive the world with our brain and how it really is. Furthermore, this difference is growing bigger as we discover more and more stuff about the world, especially about the behavior of very large things (as in astronomy) and very small things (as in quantum mechanics).
The reason for this is quite simple: Never in out evolutionary history have we had to knowingly deal with those things in order to survive. We have never really struggled with electrons, quarks, black holes and galaxies. For all we know, a piece of rock is “rock solid”, and not over 99% emptiness, which is the true situation. For all we care, when we push our finger into it, it stops our finger from getting inside. We don’t really feel it as an electromagnetic repel between many particles.
This ever-growing difference also produces the modern tension between science and religion(s). Most ancient beliefs were formed at times when we knew very little about the real world. While our brain is still the same, we now know a hell of a lot more, so to speak.
Our brain must assign reasons and conscious intentions to actions, even when the laws of nature don’t. Our brain must find interesting patterns in everything, even when in practice things are rather random. All of these feelings and behaviors have been crucial to our survival for millions of years, so we have been evolved into creatures that embrace them. What’s more “reasonable” for the human mind than thinking of a mighty god who created all this complexity around us, even while we know the true story is completely different.
This is what makes a great scientist nowadays. He or she knows to distinguish between feelings and knowledge. Intuitively I feel there is no way for an “eye” to evolve over time into its present state. In practice, I know it has, since this fact is backed up by evidence.