If there's already a server on port 80, you can run it on a different port:
java -cp fitnesse.jar -p 8080 fitnesse.FitNesse
Unix requires root privileges to run on ports below 1024 so you should probably run it on 8080 or some such anyway.
On Unix you'll probably need to chmod +x or use source to run it because zip files don't preserve Unix permissions.