I've noticed in all Gal Civ II versions sonce the 1.00 release version that the Galactic Privateer "wonder" protects trade ships from being attacked by single enemy ships, but that fleets are able to successfully attack and destroy my trade ships.

And, on a related note, the AI doesn't seem to be able to deal with the fact that their single ships can't attack my trade ships when I have the Galactic Privateer, so they'll follow my trade vessles and try to attack them anyway (without success) for quite a while until someonthing else grabs their interest, or I destroy them.