People have been arguing about gods and religions for a long time. Science, when it evolved from natural philosophy, added a new wrinkle to these age-old arguments, a new possibility, no gods at all. Those early natural philosophers weren't looking to do this; they were looking to see how their gods ran the world, they were looking for God. But, if you think about the modern God, then you will realise that we can never really find God in nature. Doing so would destroy free-will.
If you strip most modern religions to their essence, it basically comes down to: freely choose to worship God and you will receive salvation in the afterlife. The hows and whys of worship and the nature of salvation may vary, but the underlying message is about the same. People have to make the choice to worship. For most of human existence, this has been a choice between gods. Now, with the advent of science, it is a choice between God and a godless natural existence. And yet, so many people are still trying to prove that God exists, even though that proof would then destroy people's ability to chose. After all, if you knew for a fact that God existed, and that failure to worship would result in damnation, then your choice is going to be very biased. It would not be impossible to chose to not worship, and I've made an argument for it here, but it would be a hard choice. Because of this, if God wanted to maintain free choice, He has every reason to make proof of His existence impossible to get.
How would God ensure that there was never any proof of His existence? Well, there are two possibilities: create nature such that all things come into being through natural means, or create natural means along-side all creations. The first method would be the ultimate in a philosopher's God, a God that created the path for all things at the moment of original creation. It would be a single burst of creation where everything follows on its own path without any further meddling. The second method would involve, with each act of creation, creating a second natural path where that creation could also happen without intervention. Some may think this deceitful but it really isn't. God merely creates two alternatives, both worthy of belief: created by God or created by nature. This choice allows free will to happen. While the first possibility, that of a philosopher's God, is more rational, the second does allow for people that maintain the literal truth of holy scripture or traditions.
Thus, we reach a point where science is in the business of discovering the natural processes that led to the world as we observe it. Science attempts to describe nature, without God. Now, for this to happen, it does not matter if we exist in a godless universe, or if God created a universe that operates without further meddling, or if God creates natural processes alongside each act of creation. The result is the same; science is attempting to discover these natural processes. Discovering these natural processes will say nothing about the existence of God; if God exists, He would have created these processes along with everything else.
Nietzsche proclaimed that God is dead. In actuality, it was the birth of true free-will. Humans finally reached a point where they could reasonably consider a world without God. Before, choice was limited to this god or that god. After, the choice became God or no God. Science has given us this choice; it has given us true free-will.
There can be no proof of God's existence; there can be no proof that God does not exist. If scientists look hard enough, they will discover natural processes for every observable phenomenon. We, as individuals, will have to decide if we are going to worship God or not; we will have to make this decision without any proof. Worshiping God takes a leap of faith, an act of free will. How could it be otherwise?