It depends on your distance and terrain.
For shorter urban rides, flats may be better.
For longer rides, drops give you more variety of hand positions.
Note that flats can be just as aerodynamic if they are positioned low. On a drop bar, the normal cruising position is on the brake levers, the lower drops are used for downhill, headwinds and better braking.
Personally I prefer drops but I go for shallow drops rather than deep ones.
Other factors to consider on a commuting road bike:
Tyre clearance,
Rack and fender eyelet fixings on the frame.