The luciferase signal produced by transfected cells is too weak to be detect by Flow cytometry.  The cell would need to be immobilized in order to detect signal which defeats the purpose of flow cytometry.  Traditionally, cells emit between 10 and 1000 photons/sec.  With fluorescence this is in > 1M ph/s.  Most researchers will look into dual reporters with a luciferase for in vivo imaging and a fluorescent protein for in vitro purposes. A good reference is:
Construction and validation of improved triple fusion reporter gene vectors for molecular imaging of living subjects.
Ray P, Tsien R, Gambhir SS. Cancer Res. 2007 Apr 1;67(7):3085-93.

Links to Reporter Reagent Resources