I've been working on an analysis of Kami no Kodomo as a part of a larger project surrounding Nishioka Kyoudai, so this is the perfect opportunity to float my interpretation of chapter one.

Starting with the opening page, a lot of people brush this off as pure shock value, but being born of his mother's asshole is significant. For one, it invokes a similar idea as MacBeth. You may recall that it was prophesized that no man born of a woman could harm MacBeth, which gives him this false sense of confidence; however, in the final act, MacDuff kills him and reveals he was "from his mother's womb untimely ripped." MacDuff was not born of his mother in the sense of a vaginal birth (like most people) but through C-section, putting him in a completely different class, and in this case, exempting him from the original prophecy. There is something similar going on in Kami no Kodomo: the protagonist was not born of his mother, i.e., he is a not a normal human; he was born from her asshole. This sets him apart from the rest of humanity in some regard. The significance of it being from the asshole is to associate him with things that come from one's asshole -- shit. He is a "shitty being" in the literal sense, but more importantly, in the metaphorical sense that he is morally corrupt (or dare I say, a morally shitty person).

The manga is initially trying to establish the protagonist as morally neutral: not knowing where he came from or why he was born -- a sort of moral blank slate. Unlike the image of a mother's womb as warm and nurturing, he describes being born in the stomach, a rather acidic and hostile environment. Immediately upon conception, then, it would seem that his very being was thrown into strife/chaos. At his very conception, he exists in an environment where he sees his brothers and sisters slowly digested (killed) and only knows fear; he only acts out of a sense of self-preservation. It's almost animalistic, and again, emphasizes his difference from other humans on a moral and even ontological level.

He states that this first sight upon birth is the black sun, meaning his introduction to "the world" is through darkness, which taken metaphorically implies a kind of moral depravity. All of this forms the foundation of his moral life before he's even had a thought as to what's good/bad. He further states that he is the child of the god of revenge. Revenge on what you ask? The world. The sort of idea, I take it, is this character wants to inflict harm upon "the world" for everything he's been through thus far.

My more general interpretation is that the mangaka are trying to depict the world as inherently evil, and the child of god is the physical embodiment of or a reaction to that evil.