Student or Learner
How do you say when you notice some guy's trousers' zipper is open?
Do you say "Close your zipper!" or "Examine your zipper" or just "zip it up"?
Fly (clothing) - Wikipedia, the free encyclopedia
"Undone" means "not done up" or "not zipped up" (not closed).
"You're flying low" is not quite slang, but certainly idiomatic. It's a sort of pun on the word "fly" (as above). If a plane is flying low, then it's very close to the ground. In the same way, the little metal toggle on the zip is closer to the ground than it should be, because it hasn't been pulled up to the top.
In AmE we would say that your fly is open. Or your zipper's down.
I have a feeling that in BrE it was originally just "Your fly's undone" or "Your fly's open" but at some point "fly's" was turned into (misheard as?) "flies" which is why the "are" was added.