Aside from cutting down on brigand appearances (something some people aren't convinced about), there are 2 main uses for forts.
1) Protection / Buffer.
2) Luring Enemy into action
I tend to use forts extensively. I place them on roads between settlements so that an infantry unit travelling from one settlement to another can reach the relative safety of a fort at the end of each turn before reaching their destination. It's not always possible to wait until you have a large stack of units to move, and when there possible dangers nearby, giving small numbers of units a chance to hide behind walls between turns isn't a bad idea. A single unit of miltia, or some other depleted unit is enough to maintain the forts when they're otherwise not in use. Forts can also be used as rally points: keep sending units to them until you have a large enough army to move on. When brigands show up in large numbers in the middle of your empire where you have only small garrisons, the network of forts once again comes into play, providing a safer means to move your reactionary force to meet the invaders.
The AI is also regularly intrigued by forts and will attempt to besiege them whenever it thinks it can take them with a larger army. You can use this to your advantage by luring the enemy to attack your fort, and then you send a prepared army from another fort or nearby settlement to take on the besiegers. Quite often the enemy will have several large stacks close together in a region, and leaving your army in the open or directly attacking the enemy leads to a battle against many stacks at once. A manned fort often draws a single enemy stack away so you can fight one stack at once.
In my Julii campaign, civil war had erupted and I held Carthage with a single army and a few mercenaries in another fort. The Scipii held the surrounding settlements and had several large stacks not far away. To prevent being overrun as reinforcements would be slow and piecemeal in arriving from the sea, I built a fort to the West of Carthage to slow down the Scipii coming the west, and another I built north of the bridge below Carthage to prevent Carthage being assaulted directly from the south. I beat a few Scipii forces, then moved my army further south towards their own settlement and built a fort there. The army in the fort was regularly attacked by the Scipii, but it easily beat off army after army of the blue clothed Romans. Replacements were moved every turn from Carthage to the nearby southern fort, and then on to the fort held in hostile territory. When the main army wasn't attacked, the other forts were, but reinforcements could come from either Carthage itself, or from other forts not currently under attack. Using this tactic, one army took the nearby Scipii settlements and killed several stacks of Romans and Carthage never came under direct assault. The one time I didn't use the forts for cover, I ended up being forced back. Forts in hostile territory can really aid your survival rate - especially if you make sure you have some onagers and archers in them!
(Btw: The AI is so atrocious during sieges that I don't build large or epic stone walls, and having them attack forts at least gives them some hope instead of suiciding themselves at stone walls like the stupid cretins they are.)
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