This is going into military strategy and theorycraft, so i'm not sure how effective Civ4 accomplishes this. But basically if I had to use forts, I would use them similar to the
Hedgehog Defense against your blitzkrieg that simply goes past the fortified position. By stationing
a few units in forts and having your forces go past, I will be able to continue fighting your flanks from the fort. If you stagment your forces, or lag a few behind, the units in the fort will be able to threaten them.
Ex. I have a fort deployed some tiles away from my city. Your forces simply bypass the fort - there aren't really a lot of units on the fort anyways - and move to attack the city. However, if your forces become stagmented (slower movements, wasted movement points, etc.), or reinforcements are arriving, the units in my fort will be able to threaten those units and cause more casualties. This becomes even more effective if you have large tracks of land to invade and I have multiple forts scattered across the invasion path.
However, this is far from the perfect strategy. You can simple trade time and a defense bonus to erradicate each fort enroute, but by accomplishing that your blitzkrieg is slowed down and I am given more time to reinforce. Also, you can simply handle your units so that they are not vulnerable to flanks, but then you risk the chance of collateral damage. And, in a 1:1 fight you would most likely win since I have given away units from my defense line to set up the forts.
Again, this is all theory and may not even work in Civ4. But if it does, it could provide some use of forts.
(First post!)