Each of the three letters could expand to a longer word than our heroes use in their verbal shorthand. Say, U = UFP, S = Starfleet, S = Starship. That'd be a complete and logical expansion; mere "United Starfleet Starship" leaves it a bit short IMHO. Although it does nicely suggest that the UFP Starfleet might be the result of the unification of several other starfleets from the member cultures.
It doesn't make sense that the U stands for UFP, because there have been ships that belong to the UFP that use the "SS" registry only (http://memory-alpha.org/wiki/SS_(registry)) ... of course, that's assuming that "SS" means the same thing that it does as in "USS".