There are a lot of stories in the Bible. They are many of them good. There are also accounts in the Bible. The historical validity of accounts can be debated, but stories are stories. Where does the desire come from that they be literally true? Where in the Bible does it tell us that we are supposed to take the creation story as literaly true (and if we are, which of the two should we take?). Where does it say that Job is any more than a morality play? Where does it say that Jonah must have survived in the belly of a 'fish' or else the entire premise of Judaism and Christianity is invalidated? We don't send archaeologists hunting for prodigal sons or looking for houses built on sand and rocks. It seems that it misses the point a little to do so.
I suspect that part of it is that Christians don't actually read the bible in large numbers anymore. As recent surveys attest, they aren't even more knowledgeable on their own dogma than unbelievers are. Their religious teachings are coming directly from figures of authority, the communities that they trust, and the ideas in their head that they fill in the gaps in their knowledge in with.
Lets face it, the bible is a very confusing book. Several translations later, it still contains archaic language, strange word usage, grammatical confusion, and references to cultures that are thousands of years old. Theologians analyze all of this and come to the table with a greater wealth of understanding. In looking at the text with educated eyes, it becomes obvious that the bible is not a literalist account due to the style of its portrayal. They see the nuance and, despite the faith they usually possess, do not delude themselves into washing away the layers of complexity in favor of a more simplistic understanding.
There are of course varying degrees of understanding and literalism. Young Earth Creationists are on the far end of the spectrum as they seem to believe every single word of the bible (even then the ones they haven't read) is the divine, inspired truth according to the Almighty God. There's no reaching these people: they believe words committed to writing by anonymous figures thousands of years ago over active investigations into the nature of the earth and the universe which are replicable, reputable, and numerous. Thankfully, they do not seem to be the norm in the greater whole of society.
Getting your science from your bible is incredibly backward, just as getting your theology from your science is an abuse of the intent and purpose of science. There will always be margins that science cannot touch for god to dwell in, because the more that we discover through empiricism, the more questions that arise. Even if we manage to experimentally verify and understand theories on abiogenesis (which has not yet happened), there will still be questions about the origin of the matter that became life and the universe as a whole. The ad hoc hypothesis of the soul adds an additional degree of complexity that science will probably never be able to touch -- the idea of dividing reality between the physical and metaphysical is as unprovably absurd from an empirical viewpoint as it is completely immune to scrutiny.
What it all comes down to is that the religious feel threatened because science has succeeded in creating models that explain reality without the need for god. They assume that this constitutes an attack on god: it's not. Science endeavors to understand the universe using observable, independently verifiable, concrete evidence. That is not the realm of god; of course science's theories will never incorporate a deity.
What this says about the existence of god is not a scientific question, but a religious one. In that way, this is a conflict of atheism vs. theism, dragging science into the fight does no good.