The fleet command is one of two things I am somewhat competent at in this game, with the other being event trading.
Fleet commands are mostly for general things that you want done rather then like in a RTS where you want your guys to do something exact.
I always order my fleet to capture the point on the map, as their bonuses and extra command points are very very helpful.
I always order escorts for my most valuable ships, and while this does put weaker frigates in danger I mostly consider them to be expendable, lashers I believe they are called can be considered to be expendable when compared to a cruiser.
Ordering attacks on prime enemy ships can be a good way of convincing the AI to try and focus fire when it is able. Rally points if I remember correctly are a good way of getting some ships to congregate for some purpose that escapes me for the moment. (I think for stashing away carriers?)
But the comments in this thread are correct that in the case of highly manoeuvrable craft, escort duty can be troubleshoot when the captain needs to disengage and vent flux.
Now If only I could actually pilot worth a damn, then fleet commands would be even better as my fleet could stick together while I gut the enemy support ships.