There's a pretty comprehensive guide to forts in the strategy articles section.
They have a few niche uses. Airbases to augment your cities. Naval canals to bisect continents instead of going the long way around. Defensive emplacements at chokepoints - note that you can't bombard forts, so you always get a 25% defensive bonus with them. Built on a forested hill they are pretty impregnable, although how often do you find a one-tile chokepoint on a map? Rarely.
One of the better things about forts is that they are resistant to air attack, so if you use them to hook up a resource they can be hard to remove with fighters or bombers (much tougher than an oilwell, for instance).
Good points, I use many forts in the late game as airbases and also as a refuge for ships when my cities are far apart, that lets me move up and down the coast without losses or escorts.
Earlier in the game I find that a fort on a forested hill can be a very useful strongpoint and it doesn't have to be a chokepoint blocking movement. I use the fort as a safe base to harass an enemy SoD, even if they just march past it. A single longbow on a forested hill with a fort can protect against a SoD of 20 (maces, knights, cats etc). In the fort (make sure to have a road leading to the hill) I can move my own cats and HAs and launch weakening attacks against the SoD and then finish it off with melee troops. My wounded troops are safe from counter attack and can heal ready for the next invasion.
I have done this against Monty during a defensive war that lasted 1000 years

(300AD onwards). I gained a huge number of GG points and killed loads of axes, jags and cats with an exchange rate of something like 5 hammers to 1. I refused to accept peace and he kept sending mini SoDs of 8 units or so. My fort had a couple of CG archers and eventually I built 20 axemen to launch the weakening attacks, some of which gained a lot of promotions. One of my chariots reached 26 exp and was given the honorary name Aztec Axe Killer after he killed so many.

Probably half of Monty's losses came in battles adjacent to the hill fort. Not once did he try to attack the archers and later longbows stationed there. Using the fort as the lynchpin of my defence meant I could continue to research and develop while holding off Monty's attacks with ease. Although it wasn't a chokepoint and he could move freely both sides, in fact he followed a route past it each time, as I left a city with a weak garrison to entice him to destruction. Defensive wars like that cause the AI to spam units but the attrition stops the AI building up a large and unmanageable SoD.
Another use of forts is to make a "Northwest Passage" line of forts through the tundra in the top or bottom of the map when ice blocks ships sailing around a continent. Ships can pass through a fort that has own culture and is next to either water or ice covered water. That can sometimes be 10 forts in a chain and is very useful allowing naval forces to be shifted from one ocean to another without a lengthy detour. It is something constructive to do with workers once all the lumbermills and railroads have been built.