Greece to Africa by ship?

At this time (February 2013) there is no direct ferry from Greece to Africa. The reason is that there is no demand for such a service. There are plenty of ferry connections between Europe and Northern Africa. For instance, Marseille has convenient connections with Tunisia, Algeria and Morocco. There is a big community with immigrants from these countries in France. And there is trade going on between these countries. Hence there is a demand for such a service. In Spain and Italy you also have such communities, albeit smaller than in France. Spain is geographically close to Morocco and Algeria, and well connected to the North of Europe.

But is there a big demand for a service between Greece and Egypt? Is there a big enough Greek community in Egypt, or a big enough community of Egyptians in Greece? I don't think so. Moreover, the road connections from Northern Europe to Greece are not so good. A ferry from Venice to Egypt, as there has been one (see @gerrit's post), makes more sense. It can capture the demand from the more Northern part in Europe. Venice is well connected to the European road network. Nevertheless, as the situation in Egypt is rather precarious, the demand for such a ferry connection to Egypt is pretty weak.

This being said, it is possible to travel by boat and train from Greece to Morocco or Tunisia via Italy. No need to travel via Malta! There is a company which is running ferries from Civitavecchia to Tunis, Salerno to Tunis and Livorno to Tanger. There is another company operating a ferry between Genova and Tunis.

If you are interested in Tunisia, travel by ferry from Greece to Brindisi or Bari. Take a train to Salerno or Civitavecchia and then the ferry to Tunisia.

If you plan to travel via Genova, you can take a ferry from Greece to Venice and then continue from there by train.

If you are interested in Morocco, you can also travel from Greece to Venice, and then by train from Venice to Livorno.