That assumes that it did indeed come from nothing, but I believe at least some current theories do not make this assumption. KCJaysFan would probably be able to explain it better than I can though.
I believe one of the theories (based on string theory) suggest that it started as a 9 dimensional string with confined dimensions of equal size. Interactions with strings wound in the opposite direction (anti-strings) caused the string to stop confining three of those dimensions (in a process similar to matter/antimatter reactions), which released the dimensions and allowed them to expand outwards. A second theory suggests that the universe was created by a collision between two infinite 3-branes (structures containing 3 out of a certain number of allowable, in this case infinite, dimensions I think. This is getting way outside my comfort area). The energy generated by the collision creates the construct of the universe, pushing the branes apart. The resulting universe goes through phases, beginning with the big bang, then a period dominated by radiation, then matter (our period), then dark energy, then a contraction phase.
Like I said though, KCJaysFan may be able to better explain it / correct me on it.
Regardless, I don't have a problem with (serious) religion as I think a lot of people need to have something to believe in. Without that, society would probably crumble. That doesn't mean that everyone needs it. It doesn't mean that if you believe in these theories you can't also believe in God. My personal opinion is that if I have to believe in something that is essentially eternal (either by definition or by operating outside the laws of our universe), that I choose to believe there is some kind of intelligence behind it. I don't however believe that everything that happens in day to day life does so for some greater purpose.