I've always felt that F.L.Y. was a weird name, especially since the park had moved away from English names for things since Black Mamba in 2006. Since then, all their names have always seemed to be non-English words which make thematic sense for the individual rides and areas.
In my opinion, Fliegen (German for fly) sounds better than Fly, so it is a very odd choice. Like Lofty says, it must surely be an abbreviation for something, presumably German.
I've always lived in hope that F.L.Y. was simply a project / advertising name to get the point across that it's a flying coaster, and there would be a name announcement in the future. Obviously with the fight to keep the name that doesn't appear to be the plan...though I guess it's possible that may just happen!