You need to make sure that the directory was created with a non-root user.
I also recommend uncommenting the user_allow_other line in /etc/fuse.conf, and then adding an entry in /etc/fstab that mounts it as the user that will need to access it (though the group must be fuse), like so:
afpfs#afp://USER:PASS@afp.host.com/directory/ /media/dir fuse user=USER,group=fuse 0 0
Now you should be able to do sudo mount /media/dir and be able to access it.