It is the nature of forts that they are of limited use or of use for a limited period of time. They are
strategic rather than
tactical structures. They are intended to fortify a shakey border or to reinforce defenses against an aggressive and unpredictable enemy. If you are working to expand your territory you
will eventually expand beyond them.
I rarely use forts, mostly because they generally take so long to build (again, strategy v. tactics). I find my
need for them usually coincides with a period of infrastructure building (e.g. freshly conquered territory). I don't have the worker capacity to build forts
and clean damage, convert irrigation to mines (the AI is irrrigation happy . . .) etc. I have to make due with a fortified stack of defensive & artillary units.
I have used them well only once or twice (although I have accidentally set workers to to build forts instead of plant forrest

a time or three). Most notably in one game to box in the Zulu with whom I shared a short mountainous southern border. One city that defined the border was my source of a key strat resource and a lux. Aside form being a pain in my a** there was NO reason to go to war with the Zulu. The closest three cities were useless and had no resources I needed. I was going there eventually since the rest of the continent was beyond them, but there was only one civ left to my north that was a better target first. I was gearing up to take them out and the Zulu kept making feints on my city. I really did not want to get involved with a war with them, so a chain of forts allowed me to protect myself to the south with minimal defensive troops. Sure enough, as soon as I was deep into war in the north, the Zulu made a serious move.
Aside from this I have only used them for isthmus controll, and even then not often.