The answer to this is more complicated than it first appears!  It is thought in many circles to stand for Raleigh-Durham United, reflecting increased partnership between the cities, something they are both keen to emphasize.  At least this is what some people say.  But it is also said that this is not the case at all, that the 'U' was simply added by the FAA when the airport was given its four letter code, KRDU.  Despite extensive research, it is really not clear which of these answers is correct!