Specializing in supporting other Sea and Copter units, Cruisers are uncommonly built units with a limited range of targets.
The primary function of a Cruiser is to protect other Naval Units from Subs. Cruisers (along with other Subs) are the only units capable of attacking a submerged Sub. Cruisers deal high damage to Subs with their missiles, and take little damage from Subs, even if the Sub attacks at full HP. The Cruiser may also use its missiles to attack Black Boats and Carriers, but will do mediocre damage to Black Boats and next to no damage to Carriers. Cruisers cannot attack Battleships, Landers, or other Cruisers.
The second use of a Cruiser is to use its Secondary weapon to fight Air units. The Cruiser's Anti-Air gun will deal very high damage to Copters and Stealths, and moderate damage to Fighters and Bombers. Care must be taken with the Cruiser around Air units, as B-Copters and Bombers both do high damage to Cruisers relative to their cost, and Cruisers cannot defend themselves against hidden Stealths. Due to the high movement constraints that come with Sea units as well as the generally high cost of the Cruiser, Cruisers typically make very poor anti-air units, and should be avoided for this purpose unless no other option is available.
The last, and often forgotten, function of Cruisers is their ability to carry and transport up to two B-Copter or T-Copter units. Any Copter loaded on a Cruiser will have its Fuel and Ammo restored at the start of the day, and will be protected from harm as long as the Cruiser is not destroyed. If a Cruiser is sunk, however, any units it is carrying will be instantly destroyed as well, so do not keep Copters on board for too long.
As sea combat is hardly ideal in AWBW, Cruisers are rarely seen units. If the map permits cruiser use, however, they are typically easy dealt with. B-Copters, despite being only half the cost, still deal moderately high damage and go even with Cruisers if they get the first strike, making them very cost efficient counters. Bombers and Battleships will also likely instantly destroy a Cruiser in most situations if they are able to get the first strike. All Land Indirect Combat units deal reasonably high damage to Cruisers, but Land Direct Combat units will deal minimal damage to them.
When using Subs, bear in mind that the Cruiser will need either have a friendly unit or itself adjacent to the Sub to be able to attack it. If your Sub is not adjacent to any enemy units, the Cruiser cannot attack the Sub on its own. Shielding a Sub may be beneficial if you feel the enemy may find and attack it soon, as Cruisers are generally harmless towards other Naval Units.
Generally speaking, Cruisers are low priority targets, and can prove to be detrimental to attack as they will quickly fill your opponent's CO Power Bar when attacked. Unless they are directly threatening a nearby Air Unit or Sub, they are safe to ignore.