For protection, Jerusalem in ancient times was a walled city.  The present wall around the Old City of Jerusalem has been there at least from the 1800s, and sections from ancient times.  The gates of this wall are no longer locked at night.  But between Palestinian and Israeli villages there is now a security fence (only 3% is wall).  Parts of the Security Fence are shown in the pictures below from Mary Malone's 2008 trip.  The fence is there to protect the Israelis from terrorists. 

The official statement from the State of Israel, "Terrorism has been defined throughout the international community as a crime against humanity.  As such, the State of Israel not only has the right but also the obligation to do everything in its power to lessen the impact and scope of terrorism on the citizens of Israel.  The Security Fence is an operational concept conceived by the Israeli Defense Establishment in order to reduce the number of terrorist attacks whether in the form of explosive- rigged vehicles or in the form of suicide bombers."

Many of the questions and concerns of the fence are addressed in the Israel Defense Forces (IDF) video:

Fence Against Terror (click to view)

(Video - Israel Defense Forces   Spokesperson production).