If you give them a ship, then you have to challenge the ship. The other option is letting them effectively have a walkover of whatever is on the ground. This will be fun for a bit, then get boring. Also, put up an enemy who thinks smart, and figures out a way to disable the warship without fighting it. Dumb enemies would normally have been weeded out in BT's constant war, so have the players feel like they just got dropped into a shark pool. Smart enemies deal with large threats. The players just became one of those large threats due to the warship. Have enemy spy teams change targeting coordinates that are transmitted, so the Warship does orbital fire on the players, rather than in front. Have missiles get launched around the planet the long way, and arrive at the Warship's coordinates at terminal velocity. If the missile miss the warship, they slam into the atmosphere headed towards the PC force.
Also, while the players are busy in one location with the warship, have the enemy do objective raids behind the line, screwing up the PCs' supply shipments, so their Warship (which is mainly NAC/NGauss/Missile armed) has to make each shot count. Supply shipments will get raided, fighter probes keep the Warship at general quarters (degrading the effective rating due to lack of sleep), even having an enemy warship stop by are all sorts of fun that can occur.
Now what you could do is have a Naval Captain who will give them preference in fire support, but that also means they will be heading into areas that need fire support of that magnitude. Also, if the warship has to divert to support someone else, there are going to be a lot of very angry enemy units free to open fire.
The players should also be using their contacts to keep the critical supplies open. Hydrogen fuel is easy to get, but repair components for a Warship transit drive will be much harder to come by. Replacement parts for a PPC are everywhere, ERPPC not so much, but HNPPC components almost have to be custom made. Ditto for Naval grade missiles, NAC ammo, NGauss coils, compact core components (let alone annual maintenance requirements).
They might have the ship, but some noble (getting jealous) decides to bump their Compact core annual refit down a few notches (accidentally keying a 5 instead of a 2 thanks to the number pad), so their Warship has to sit in orbit for several months, waiting. Getting the priority bumped back up will be a fun exercise to find the right people who can change the paperwork, or wind up owing several people favors. An enemy can also wait until it is in refit, and launch a bearings-only missile from a Dropship in-system, timed to hit the Warship when it has the core exposed. Presto, instant monitor.