And God could have used allegories. But fundamentalists don't like that one. Many religions have a birth (Creation story in the Christian faith's case) and a rebirth (the flood wipes it out and voila--new world) story. Just following the typical pattern of religious stories.
Biblical literalists have painted themselves into a corner. They can't admit any fallacies in their sacred tome or they will also have to concede that any other part of it may be faulty. Furthermore they must stick with the magical story of a worldwide flood and any other fantastic stories found in the Bible, because sans magic it becomes far to easy to ask "why was a supernatural being necessary in that story?"
A woldwide flood --where all animals were mystically transported from their natural habitat to a central location and then mystically transported back, where all of the different species could cohabitate, where they had no need for food or fresh water, and where the handful of people onboard the vessel could adequately perform all of the functions necessary for sailing, navigating, and taking care of the animals--requires a divine hand. A local flood where some old bearded dude makes a boat so that his own livestock won't perish requires no divine hand. Heck, things like that happen all the time.
Of course God could have wanted to avoid confusion and tell us how things actually happened,but atheists and agnostics don't like that one.