OK - i agree it sounds dumb in the movie. However, I think Cameron (or whoever) was trying to be somewhat scientific. This is a material/compound that makes mountains float. You can easily see where it might have been first discovered in a science lab and deemed "unobtanium", only to later be found to exist in mass quantities on another planet. The name would've undoubtably stuck.
I realize that I shouldn't defend the movie for it's "science", but I just don't see it as a big deal. (I honestly shouldn't defend the movie at all. I saw it once when it first came out and haven't seen it since. I enjoyed it OK at the time...more bothered by the generic "Cameron-ness" of it than that it ripped off Dances with Wolves or Pocahontas.