I must admit, due to their expense, and the fact they tend to be primaried and die alot, you don't often see these in fleets so I have limited experience with them.
I can not fly them myself, but I know several pilots who do.
The Nighthawk (Caldari Command ship) can fit a rediculous tank for a ship its size. I've seen a buddy in a nighthawk tanking a lvl 5 mission solo, admittedly the guy had implants and it was faction fit, he was at range and going fast, but it can be done.
Generally though the abilities of a command ship lie in leadership bonuses and the warefare links, Sleipnir tends to be the one you see if you see any in PVP use,(I've come accross 2 in the year since I've been back) one in a gang of 10 and the other in a gang of about 25.
The small 10 man fleet he must of had a maneuverability gang link, as there was a Vagabond doing about 10 or 11k a second. There effect is very subjective, but that 10 man fleet got ganked by 40-45 of us, and they lasted alot longer than they should have to us. Some may say that's down to good skills and piloting, and maybe it was, but I'm thinking the bonuses given by the Sleipnir were what was keeping them alive, because when we finally killed it they all ran away.
These are both Field command ships which are great for passing on bonuses, with ample but not exactly heavy DPS when fit out for fleets, best used for small gangs of 1 to 2 squads!
A real Fleet Command ship like the Claymore gives huge bonuses to fleets, problem is keeping them alive.
However I believe the warefare links work as long as you are in system with your fleet.
If this is the case, this may be why you don't see them in battle, as they are tucked away in a safe spot somewhere nice...
Can anyone clarify if these ships need to be on Grid with you to work?
Basically though it is horses for courses.
As I recall also (not 100% sure on this), each fleet command ship, has a specific additional bonus to its race special warfare link, as well as just a bonus to using them.
Amarr to the Armour one
Caldari to the Shield one
Matari to the speed one
Gallente to the Targeting one.