Fleet Command is essential to group PVP - by coordinating the actions of your fleet centrally you will be far more effective as a fighting force.
At a basic level, Fleet Command may simply mean making sure all of your gang members are shooting the same target (i.e. target calling). With a bit more work, it can allow your fleet to perform coordinated actions that drastically increase its effectiveness when compared to a group of individual ships.
The articles below discuss various aspects of commanding a fleet in PVP.