too intelligent to actually be intelligent?

Survival of the fittest doesn't mean only the organisms with the perfect characteristics survive. That's nonsense. Survival of the fittest simply means the organisms with the best available options for the given environment survive.For example, the human eye is an imperfect design. Compared to the octopus's eye, it's a crappy design. But obviously, I can still drive around without wearing my prescription glasses... during the day at least.

I don't think atheists rejects all things that are not physical. I certainly don't reject the idea that my mind exists. Computer softwares are also non-physical and i fully recognize their existence.I think what you are really asking is why do I, as an atheist, accept the existence of some non-physical things, like minds and computer softwares, while rejecting the existence of other non-physical things, like gods, angels, and immaterial pink unicorns? That, the answer is simple. I have no reason to believe in the latter group. Occam's razor. If gravity is enough to explain a projectile's behavior, then there's no need to assume flying angels pushing the projectile.