Certainly there are many Science Fiction writers who touch upon the subject of beings supreme to Man...but always Man is central in writing.
Because God does not have a story arc. If story is the conflict between desire and what stands in the way of the fulfilment of that desire, God cannot have a story arc because nothing can frustrate the desires of God.
There are, of course, stories about gods. But those gods are really supermen. They have limits. They have desires. And they have forces that frustrate their desires. Thus they have the components of a story arc, and thus also they are, for all that matters in story terms, human.
The same applies to the animals in stories like Watership Down or The Wind in the Willows. In story terms, they are human too.
As a counter-point to mbakeranalecta's answer: God can have a story arc albeit one with an obvious victor. For example: the Christian God Yahweh takes human form (with the name Jesus) in the books Matthew, Mark, Luke, and John. Since he is omnipotent there is no evenly matched opponent however there is an introduction, a goal, a journey, build up, a climax, and a resolution. There's even suspense at a few points.
Jesus had a desire (to save humanity) and antagonists (namely the pharisees) which stood in the way of the goal. Granted he was never frustrated by their attempts but certainly this qualifies as a story.
Although there are plenty of conflicts, all of them are one-sided. The trick questions given by the pharisees are easily and immediately answered. And if you read the back story (the Old Testament) you'd know that by definition (of omnipotent) God can't fail. Which forms a weird plot armor in that we know that Jesus will die but he will also always succeed (even if painful). And that no force can even slow him down with temptation and death happening exactly as expected. And this exactly what we would expect from an omnipotent main character: people stand in his way but it in no ways hinders his progress.
Stories of a utopia are about a perfect place, writing about a perfect person has some similarities. Writing about a perfect place could have a purpose of "this is the perfect place and we should strive to make our society just like it" likewise writing about a perfect person could have the purpose "this is how a perfect person acts and we should all strive to be like him".
Pretty much the only stories about a perfect person are wrapped in either religion or philosophy because generally speaking these stories aren't as popular. A lack of challenge is considered boring and of course no reader can relate to a perfect person.
My answer answers "can it be done" (yes) and "why would it be done" for a perfect all powerful main character. As for viewpoint: it exists and is called an omniscient third person narrator (whether the narrator is a god or not).
There are plenty of SFF stories which deal with deities. There's an entire Forgotten Realms (D&D) series about gods being forced to take mortal avatars and walk the earth. The Belgariad pentology by David and Leigh Eddings (and less so the sequel pentology, the Malloreon) heavily features deities as significant secondary characters. Rick Riordan writes about Greek, Egyptian, and Norse gods in his various series. This thread has many other suggestions involving deities of various religions.
If you're asking why Yahweh, the deity of the three Abrahamic religions, isn't used as a character in SFF stories, the main reason is probably what mbakeranalecta suggests: there's no character arc. Omnipotence renders a lot of plot useless. ST:TNG's Q had to have his powers removed or had some ethical obstacle in his way in order to have a story.
If you mean a singular God as prime mover, it's been done, usually as a gag rather than seriously. (For example, the grad student who is getting a failing grade on his create-a-planet lab assignment; personally I'm particularly fond of Stanislaw Lem's treatment of that in The Star Diaries where it's a matter of incompetent committee work.)
If you mean one of a pantheon of gods, it's been done many times in many ways. Tanith Lee's books about the Lord's of Darkness. The Sandman series of comics, by Neil Gaiman.
And so on, and so on.
So the premise of the question is flawed. The fact that you haven't seen it does not demonstrate that it hasn't been done. It's just harder than average to do well, for the reasons others have provided.
I have read several stories like this.
In one, humans of the future are able to use sci-fi tech to "read" any moment in the past, and use this to bring back the consciousness of those who have died. The Utopian society they returned to was, effectively, heaven. Mankind is indeed still central in this novel, but it brings about another concept for god: he/it doesn't exist YET, but will, as a culmination of OUR evolution. (Light of Other Days, Stephen Baxter).
In a similar vein is a short story I highly recommend, Asimov's, the Last Question. Oh, I found a link right to it ( it's pretty short: http://multivax.com/last_question.html)
In the Culture novels, by Ian Banks, there are super-intelligent computers, that are able to simulate entire worlds in such detail that the citizens of these simulated worlds are even granted "living-entity" status. This status prevents the more moral of these intelligences from deleting the simulation, (over which they are indeed omniscient and omnipotent), when they are done with it! Of course he also talks about simulations in THOSE simulations, and multiple "levels" of reality. To make the omnicient/God thing even more clear, one of these novels even deals with simulated hells! (Surface Detail, Ian Banks) While most of these stories DO revolve around human-like people, to make it relate-able and interesting, I would not dare to call the Culture "human-centric".
The lack of involvement of a God in Science Fiction (as opposed to, say, epic poetry) is really a bit of historical trivia--God was simply a less popular character in the times in which Science Fiction was written.
This phenomenon isn't unique to Science Fiction--not many very popular works have been written in the past few centuries with a benevolent, omniscient, omnipotent viewpoint because it's too difficult to try to resolve the Epicurean Paradox while keeping the usually quite devout masses happy because, surprise! The Epicurean Paradox is paradoxical!
The only answers I've seen continue to crop up are the idea of "optimism", that is, that this is the best God could do (Paradise Lost, Theodicy), but that idea was roundly thrashed by Voltaire, OR that God continues to allow this evil so that humanity may (depending on who you talk to) prove it's worth, build character, etc. in so many words: become stronger (kind of like how working out at the gym hurts, but it saves you future pain).
 "If God is omnipotent and omniscient, why is their evil? If he is not omnipotent, then he must be weak (and therefore not godly). If he is not omniscient, then he must be ignorant (and therefore not godly). If he is neither, why call him God? (for he must be not godly)
The answer lies in our ability to define 'God'. Note that while we talk of God, we are personifying an all-pervading aspect; and sometimes the language in which we write or speak becomes insufficient to define 'Him' [note that even in this case, 'Him' indicates that I am referring to 'God' as a male character]. So what is this aspect called 'God'? Ancient languages such as Sanskrit (of which I know a bit) talks of the concept called 'Prana' (how you pronounce it is another consideration) that leads to, and not directly is, the aspect of 'God'; and this implies both human and non-human sub-aspects. So while a story needs to be written, it is important to confine 'God' to the human characteristics (which has been already earlier pointed out), however that would not suffice given that it would seemingly not be sufficient to cover, if not conflict with, the non-human aspects. Hence, any attempt to write a story on 'God' would boil down to a lesser being of being a 'human'.
Indeed, why not?
I suspect that to be because most people don't spend a lot of time actually contemplating God or Gods in a realistic fashion.
After all, individual, group, cultural, and theological assumptions keep getting in the way, not to mention there isn't much profit perceived in such activity by most.
Simply put, most people don't actually have a clue what a real God would actually be like. Even those who can trot out a list of characteristics and may even fervently believe in a God or Gods, seldom actually apply any logic or natural conclusion effect to said characteristics and try to figure out what it means in real terms.
You also have the people who reject it out of hand based on little to no thought, others who decide it doesn't make sense and never dig into it, some who associated it with a poor experience, those who simply like to troll, and on and on.
Very rarely do you have someone who studies it thoughtfully and with an (actual) open mind, regardless of outcome.
I will give one possible example of an excellent viewpoint for a stereotypical deity which would make good writing.
Let's even use the Judaeo/Christian God as our example, as that has already been brought up.
An omniscient, omnipotent being. For the purpose of the example, let's suppose this being conceives the desire to not be alone. However automatons just won't do, that's the same as still being alone with toys.
Therefore, other beings who are agents unto themselves, who have the ability to move, to perceive, to act. Also, inherent in that, the ability to NOT do what the being wants, and a commitment to never interfere with these other being's ability to act and choose for themselves.
Second assumption for the example: purity, cleanliness, and holiness/sacredness are also typified by said being. No impure, unclean, unholy thing can exist or dwell with said being. This concept is also pretty well established, even if the nuts and bolts are debated.
With the ability to act, therefore, these other beings can commit acts which render it impossible to dwell with the original being. Therefore a method of teaching not only the knowledge of how to be pure, but a method to cleanse an impure other being is needed, and a way to teach an appreciation for the value and worth of remaining pure or regaining purity and dwelling with the original being.
And so forth. I'll stop here, but I hope my concept can be extrapolated from even this little. In recap: a God who self-limits by never interfering with the ability of mortals to choose but requires purity of all prospective dwellers, life therefore being some kind of school and test all in one, and the desire for other free agents who are capable of being pure enough to dwell with God of their own free will and choice; and you have the makings of all sorts of interesting stories with conflict and drama, successes and failures.
Omnipotence is limited by the non interference clause, and even with omniscience being able to calculate every possible outcome, the being still cannot act in an interfering way, thus allowing for drama and conflict and challenge even from a divine viewpoint.
With respect to the `no story arc' issue, there is a certain amount of latitude in frustrating the desires of an omnipotent being, as per the following dialogue by the logician Raymond M. Smullyan:
There's further discussion on this in Douglas Hofstadter's book `Metamagical Themas'.