I don't recall a scientist EVER saying the universe came from nothing? Matter may have existed as energy before the big bang (due to the conservation of mass-energy), the energy may have become mass, the mass becomes infinitely dense, it goes bang, the universe as we know it is born.
I believe a more detailed and explained version of what I just said is written in the book "Atheist Universe". It's only a hypothesis at this point but that doesn't mean that just because we don't know something that we need a god of the gaps to fill it in. You see, the difference between religion and science is...
Religion: We don't know, god did it.
Science: We don't know, we will actively search and study until we do.