First of all, my internal knowledge is nowhere near the capacity to understanding the logistics and science behind the Big Bang Theory. It's so confusing in so many aspects.
But where did the matter come from? Who knows. No science can explain how something came from nothingness. Not even religion has been able to explain how something has come from nothingness.
I simply ask one question. Which is more plausible: That unintelligent matter spontaneously came into existence or complex/intelligent matter spontaneously came into existence? Which do you think is more plausible in this kanundrum(don't know how to spell that but it sounds good here).
Personally I think it's more plausible and easier for soemthing less complex to spontaneously arise than something that is much further complex.
Going with that how it arose, who knows. We've yet to understand the full mysteries of our universe, and we may never understand them. But do we replace ignorance with lies and myths. I think not. I think we should replace it with determination to find the truth, and also acceptance that we are only human.
