I think you've fallen into the Creationist trap. Creationist debates tend to slide into whether or not atheism is just another religious faith and reduce it to that. As if it is two different sides debating meta-physics.
The difference is that atheism doesn't make claims of the sort and can't. It's not what atheism is. Atheism is simply the rejection of one particular religious theory. Usually Christianity in these western parts. A Christian is per definition an atheist as far as Islam is concerned. Atheism is as much a religion as not playing tennis is a sport.
But let's say atheism gets to represent the rejection of all religions. It's a huge leap to say that an atheist by default prays at the altar of science. Believing in specific scientific theories is a question of faith, and accepting scientific evidence above other types of evidence is very much a question of faith. There's no breaking the atheistic creed by believing in faith healing, unicorns and the theory of relativity... all at the same time. That's not what it means. Atheists can quite cheerfully reject both religion and all science.
But let's go along even with this. Let's for sake of argument say that being an atheist means that one thinks science is the measure of all truth. I doubt many atheists would agree, but just for the sake of it, let's do it. How does the fact that they can't explain faith healing or the origins of our universe give an ounce of credibility to any non-scientific theory? Stuff we don't know... we don't know. We can't really say anything more than that.
I hope I've managed to kill off any ideas of that atheism and theism are some kinds of binary sides to chose between. It's much more complicated than that. There's either belief systems which have complete theories of everything, (religious or not) and belief systems that accept that we don't know everything to draw such conclusions, (religious or not).
Discussions like this tend to limp along where theists and atheists attack the dumbest and most superficial ideas from each group and both sides think the other is missing the point. Those discussions doesn't go anywhere and are hardly helpful. Please guys, lets avoid it. Discussions like this always need to get broken down into specific discreet areas. Like, did Johnsson's kid get better because of a miracle, or was it just chemistry? ...or how do we know the Bible is the word of God?