Tunis: There are no overland connections from Tunis to Egypt and definitely no railway in Libya, neither are there any ferries along the coast from Tunis to Egypt as far as I know.
Ferries from Europe: In July 2001 I saw a passenger ship/ferry in Bur Said. It was bound for either Greece or Cyprus. Unfortunately I never asked and haven´t been able to obtain information about it after I came home.
Through Asia Minor: You definitely don´t have to go through neither Israel nor Palestine to go from Europe via Syria to Egypt. There are weekly night trains Istanbul-Halab (supposed to have a through car to Dimashq (Damascus) but normally hasn´t), daily day and night trains Halab-Dimashq, day trains every Monday and Thursday Dimashq - Daraa - Amman, supposed to be buses in Jordan from Amman to Aquaba and ferry across to the Aquaba Bay to Egypt.