There are two possible answers:
One is that subway service in Brooklyn was suspended completely. For instance, the A train from the Rockaways to Upper Manhattan would bypass all stations inside Brooklyn.
That however, would be greatly inconveniencing to passengers, so more likely, given the shot of soldiers lined up on a station platform when Devereaux is giving his speech, they had soldiers stationed at every station inside the borough, do random searches of passengers and their bags for explosives.