Why does science disprove God? Because natural history is inelegant. What kind of all powerful, all knowing, all benevolent God would start the world 13.8 billion years ago, wait around for ten billion years for the Earth to form, then have life evolve from single celled organisms for four billion more years, only to finally arrive at humans a few hundred thousand years ago?
What was God doing during all that time? Playing tiddlywinks?
He was omnipotent, and he chose the slowest route possible to the first interesting thing to occur in the universe -- us. Why?
He's infinitely intelligent, but he's intellectually satisfied with the dull workings of hydrogen and helium atoms for ten billion years? He's fine just watching them orbit each other in lifeless hunks of matter for nigh-eternity? It might interest humans for a few years to understand the complex dynamics of high level physics, but there's no way we'd stay excited and curious and entertained by hydrogen for ten billion years. So why is God acting like the retard of the litter, interested in doing the same thing over and over and over again? Just imagine God entertained as he pushes a bell and hears it ring over and over and over again for ten billion years. Are we supposed to respect a God like that? Pity, yes. Respect? No.
And then the all good part is just laughable. This is a God that couldn't figure out how to spare us from death and pain? From disease and natural disasters and disabilities? Humans, in their benevolence and mercy, have gone to great lengths to help others and protect them from harm or death. But God, despite being all powerful, won't even lift a finger? What a worthless wretch.
Why on Earth would God wait around four billion years for life to evolve into what he was waiting for to begin with, mankind? Why didn't He just make us to begin with and get on with things? Who the hell says "I'm going to have a coke, I guess I'll go to the fridge fifty years from now?" Once you have a goal in mind, the only elegant course is to achieve it as soon as possible. Putting it off is considered a sin -- sloth, so what term do we even use to describe a God who puts off making mankind for four billion years as he waits around for amoebae to do their thing?
God's actions aren't just mysterious, they're incomprehensible. They completely contradict what our brains say a God should be like. If God is Good, if God represents all of our virtues to their highest degree (and mind you that's what the holy books say, that God is Good and Man was made in his image, so his Good is the same as our Good, his virtues just a higher version of ours), he just would not act like natural history says He did.
Within the confines of what we know of science, that the universe is fourteen billion years old and yet we're the first sentient beings in the universe, the horrible inefficiency and inelegance of God's creation is laid bare. The Emperor Has No Clothes.
No one would Create like that. Seven days? Yes. 14 billion years? You've got to be kidding me. Why would God live a purposeless life for fourteen billion years before finally getting around to his goal in life? If God doesn't make us, what is he worth? If he doesn't rule us, judge us, monitor us, guide us, save us, etc -- what is he worth? A God of atoms is as pathetic as the atoms themselves. Any random human will have done more good in their lives than God if God doesn't help humans. So what kind of God just loiters around all that time, achieving nothing of merit or virtue, nothing to distinguish himself with, even with all that time and all that power on his hands? It's contemptible. If I were God, I would've committed seppuku in embarassment/shame for my lack of achievements after all that time. We expect kindergartners to do more in a year than what God managed with 10 billion.
The problem of evil is indeed thorny for any theist. It's hard to reconcile anything but a Devil with genetic disabilities and plagues that completely innocent people can be harmed by. But you could make all sorts of hand wavey arguments about how this is a good way to test people's mettle, and it's necessary to separate the good from the bad for your future plans in the afterlife. There's things you can do. Maybe not very convincing, but there's leeway.
The problem of inelegance, though, is just unsolvable. It's just blushing in shame complete loss of face. Your all powerful God couldn't make humans to begin with, he had to start with single celled organisms and then slowly coax them up to beings with souls over four billion years of tinkering? Come on. That's just ridiculous. Your God totally sucks. He's so weak, so feeble, so slow-minded, so just plain slow, that he's indistinguishable from blind chance making mankind all on its own.
There is room for God, but it can't be the God old religions talked about. The new God would have to be someone of limited power and resources, who did the best he/she/they could to make our universe, flaws and all. For instance, people escaping heat death by setting up the preconditions for another big bang that they calculated out would eventually contain life again, but couldn't do any better than that.
Another explanation would be that this is just a simulation, and the people doing the simulation weren't focusing on us until the computer got to the good stuff, and they were just letting things automatically play out until then. Their goal would be observing only the interesting stuff, and they could go back and forth in time freely to observe whichever aspects they were most interested in because the computer has already simulated out this universe from beginning to end. This God is slightly cooler in terms of all powerful, but certainly isn't all knowing (or the simulation would've been pointless), and most certainly isn't all benevolent, as he's willing to visit all these misfortunes on us just to satisfy a point of curiosity or desire for stimulus. It's impossible that such a God would ever intervene in our affairs, so all prayers and miracles and holy wisdom are out, which makes it as though he doesn't exist even if he does. As far as we're concerned a God like that existing makes no difference to our lives whatsoever.
The death knell of God wasn't the theory of evolution. It was the age of the Earth. In fact, Darwin only started to believe in the theory of evolution after he learned from recent discoveries in other fields that the Earth was much older than everyone previously thought. But even Darwin wasn't even remotely aware of just how old things really were. It's possible to imagine God staying busy and fulfilled and entertained setting things up over thousands of years. If evolution occurred over thousands of years, we could just be like, "well that was a weird way to do it but whatever, God knows best." Four billion years though is just inexcusable. And then when we learned that we weren't the only galaxy, and we were still receiving starlight from suns that were 13.8 billion years away, it just made a mockery of everything. 14 billion years? What the hell? How is God's plan to start things up, then get a coffee for fourteen billion years, and then sit down in his recliner and finally get to judging mankind's sins? What the hell coffee break lasts that long? For God's sake man, shit or get off the pot.
You could make the argument that the Earth was actually created only a few seconds ago, and God just made it look like the universe was 14 billion years old, that we evolved from bacteria, etc, and all the starlight was already in motion at the universe's creation. The very moment the Earth was made there were already fossils of dead organisms that never lived at all. This gets around the problem of God apparently doing nothing for 14 billion years like a complete idiot. But now you've got the biggest bastard in the universe ruling in heaven. Why the hell would he go so far to deceive us? What is the point of this gigantic charade? Who would play such a practical joke on his own creation? God is a liar? So he no longer even stands for Truth? So what makes him even remotely as good as even the least of us?
There's no answer. God is an idiot or an asshole, all because of the age of the universe. The age of the universe ruled out all religions. A creator is still possible, but such a creator is just an object of scientific curiosity, not worship. On level with us, or perhaps even beneath us, hardly our better.