You have a point. Drop the evil of everyone in the world, Noah's unusual virtue, the huge ocean going boat built in record time by one dry land farmer, forty days rain, the saving of all the animals in the world, the covering of the mountains, the first appearance of the rainbow, God's promise not to do it again, and so forth,
bring it down to a man rescuing his livestock from a bad flood while leaving the neighbors to drown,
and there's no reason to call it a fairy tale.
There's no reason to call it the story of Noah's Ark, either.
The Bible doesn't call it the story of Noah's Ark; we do. And incidentally, the boat wasn't built in record time, and it wasn't built by one man. 40 days of rain isn't so impossibly rare to believe it couldn't have happened - though evidence suggest there was certainly more to it than just rain. As for the other stuff, that gets into the core of ANY spriritual person's beliefs, and I think the root of the difference between atheists and theists.
Atheists (in general) like to characterize theists as foolish, superstitious idiots that ignore science or try to shoehorn science into their faith - and while that may certainly apply to plenty, it doesn't apply to all - and more importantly it doesn't touch on the REASON theists believe. They may indeed be foolish, superstitious, or an idiot that tries to mangle science in an effort to make it fit with their beliefs, but that is just ancillary (for most). The reason they believe is because they feel a spiritual connection to ordinary things that happen in life. They see patterns, and associate these patterns with a cause and effect that, for Christians, is described in the Bible. The countless "good stories" as you put it certainly teaches different morals, and those serve as lessons for those who hold the Bible dear. In fact, the more those lessons are born out in modern-day life, the stronger the conviction of the believer becomes. So, for most Christians, whether those stories are allegory or not is for the most part irrelevant to the way they choose to live their lives, based on the guidance provided in the Bible. The morals are valid, and the SPIRITUAL teachings are applicable to their everday life. Most Christians really don't care about a lot of the details, because for them it wouldn't matter if they were allegory or not. But that truth that gets born out in their lives, is personified as God. Perhaps the term was never meant to mean anything more than a metaphorical personification in the first place. Perhaps Moses didn't actually think he was talking to a being called God; he just used the term to apply to the things he couldn't explain. I don't actually think this to be the case, but it could be and it wouldn't have any practical implications for the modern-day Christian.
Now some, such as myself, find it a fascinating endeavor to try to put together all the different pieces, much as an archaeologist will try to put together a picture of every day ancient life. We aren't content to just follow the spiritual teachings, but we want to understand how everything came to be. We DO believe there is an actual deity that created everything, and I at least want to understand how that deity communicates to others. In the example of Noah, I think he was probably just another farmer who came from a long line of tribes and nomads that believed in a single God. They felt his presence in a great number of daily experiences (things that today we could no doubt trace back to specific scientific explanations - such as what causes a rainbow), and probably acted on such spiritual beliefs quite often - much as the tribes in other parts of the world that would connect a solar eclipse to bad crops, or a human sacrifice to good ones. In the case of the flood, there were probably a millions signs that led him to the idea that a flood was coming - possibly animals being driven from their habitats when smaller sections near the sea started flooding - unusuals winds, increased (or decreased) moisture in the air. And when the idea popped into his head that all of this meant a flood was coming - without any real causal evidence to that reality - he believe it was God speaking to him. And the story of Noah is one of faith and conviction. He continued to believe, despite the criticisms of his neighbors, and continued to prepare (he didn't let them drown btw, he tried to convince them that the flood was coming). When the flood did indeed come, it no doubt convinced him even further of the presence and reality of God.
Understandably, an atheist can read all of this and continue to not believe. And a theist will have their belief strengthened. It really just boils down to the presence or lack of faith. I understand that there are natural causes for all these things, but I believe that God created the natural causes, as well as the biological mechanisms that ultimately lead to the ideas that might pop into one's head from nowhere. I also understand that that may be all there is to it, and that there isn't a God on the outside that created everything. But it isn't what I feel, and it isn't what millions of others feel. It isn't what we believe. And insisting that things are allegory, or have natural causes, or were just superstitions, or whatever, really just all fit into this worldview anyway - so everything you are all saying as reasons why you don't believe are in fact the very reasons why I do.