No, there hasn´t been passenger ships from Italy to Egypt for a long time. When I was in Bur Said (July 2001) there was a passenger ship going to Cyprus and possibly Pireus. But it is very difficult to obtain information about ship connections to Egypt and I know no more about this ship or whether it is still running. And you cannot travel by freight ship to and from Egypt - Egyptian authorities don´t allow it!
But by car you could go through Turkey, Syria and Jordan, and by ferry from Jordan to Egypt across the Aquaba Bay.