Why does the flood myth seem to permeate cultural myth and psuedo-history? Is it just something basic we're afraid of deep down, or do scholars think that there WAS a period of flooding and that inspired much of the myths we read now.
First, I suggest taking a look at the relevant section of the FAQ.
The point I'd emphasise is that there are many thousands of myths that appear in multiple cultures: there's nothing unique about the flood myth. There's no more reason to interpret it as something hard-wired into human brains, or to imagine a historical event underlying the story, than in any other folktale. E.g. we don't conclude from the wide dispersal of the Polyphemus myth that there was once a race of one-eyed giants who liked locking people in caves.
To add to /u/rosemary85 's comment, we in the West have a confirmation bias when looking for flood stories because the Abrahamic religions and their ideological ancestors all tell a flood story. So when we see a different culture with anything even vaguely related to a flood, we emphasize the importance of that story in our understanding of the other culture because it is something to which we can relate. So, for example, Chinese mythology has stories about the flooding of the Yellow river, but it isn't the same flood story as Noah and the Ark by a long shot. Any civilization that developed around a river probably has stories relating to the flooding of that river, but what about those that didn't? Do cultures in the Sahel or Polynesia or the Atacama have flood stories? Maybe, but they aren't foundational in the same way Noah and the Ark is.