Living in an open society makes security measures much harder to develop and enforce. Until there is a specific attack on a system, there isn't much motivation to ramp up basic security measures that are more intrusive to passengers and cargo.
This 2010 GAO Report
Ferry Security Measures Have Been Implemented, but Evaluating Existing Studies Could Further Enhance Security highlights the need to do more. And, while we have not seen terrorist attacks on a ferry system here in the USA, they have occurred elsewhere in the world.
FYI, Washington state operates the largest ferry system here in the United States.
Eric Holdeman is a contributing writer for Emergency Management magazine and is the former director of the King County, Wash., Office of Emergency Management.