In the Military Museum outside Tunis there is a display showing the similarity between the current flag and that used by the Beylical government in the 19th century. The tone of the display is pride in the continuity of national identity. I suspect that during the extended period of French colonial domination, Tunisians looked back at the crescent and star on a white circle as the emblem of national sovereignty, since it had been the flag under which their last independent government had ruled. Just speculation, but it makes sense to me.
Lion is for order, ship is for freedom and balance is for justice.
Ship reminds of historical Fenician history of the country, and its today's maritime interests.