I've caught small Flounders on a minnow pattern I got from Chris Newsome's web site and Chartreuse over White Clouser.  Jeff Dubinok has a Zonked Rabbitt pattern (JD's Flounder Fly - I think it's called) in Flies Of The Chesapeake published by the Club.  I've never caught a keeper size flounder on a fly.  Interestingly, though, there are several varieties of flat fish in the Bay.  Some a real neat looking like the Hogchoker.  Requires a very small hook (#8-10)because it doesn't get big at all and has a small mouth.  Flap.