Chappy,
I would say the point is that god (despite the fact that no-one can offer a generally accepted definition of what that word means) can never be proven empirically.
As humans we quite often accept everyday things at face value, extraordinary claims require evidence. Whilst for example I would accept it if you claimed that you had a large motorbike in your garage, I would be much more skeptical if you claimed to have a large pink dragon called Doris.
You are correct there are two choices, you either believe that the universe is entirely natural or you believe that it is supernatural. Neither choice is impossible since I cannot prove that god doesn't exist I cannot entirely rule out the possibility that I am wrong, and conversely the same is true for you.
Does matter come from nothing?, science doesn't know what came 'before' the big bang. Perhaps one day we will know, all I know is that we will be constantly striving to find out in the meantime.
Why do I choose the naturalistic explanation? Because I accept that the origins of the universe are broadly as science have explained them, there is empirical proof for the big bang. If I were to accept that god did it that would mean I would have to tack on a belief in a supernatural intelligence that preceded and caused that momentous event and that this god has either always existed or popped into existence from nothing. The latter does not seem to be the most parsimonious answer. For me the latter is by far a greater leap than the naturalistic one.
I reject all gods even the nice ones. At least until I can see some empirical evidence.
All I can tell you is to THINK and not just accept every "scientific" non-explination for existance and conciousness.
All I can tell you is to carry on thinking and if having a belief helps you then fair play to you. I don't agree that any serious science is a non-explanation, it might be difficult and it might not answer all our questions but it is the best and brightest tool we have to understand the world around us.