It depends upon which tonneau cover model you have. The earlest covers had a flat piece of rubber that wrapped over the hinge. That kind could easily be replaced with a strip of rubber but you would need to remove the hinge to remove and replace the old rubber seal. Probably a good idea to use some silicone sealant when you reassemble the hinge. Disassembly may require removing screws or drilling out rivets and replacing them with screws.
If you have the later model cover (started sometime in 2002) they have a hard molded rubber cover over the hinge with short end-caps. That kind will probably have to be replaced. I don't know if Ford stocks those parts or where to get them, or what they cost? You might want to try using some kind of rubber cement to see if you can patch it that way, at least to prevent a major water leak. If you do find a replacement seal, you will have to dismantle the hinge to install the new weather seal.
...Rich