Although the crime threat is critical, most people do travel throughout San Salvador, and the U.S. Embassy Community Liaison Office (CLO) sponsors trips to outlying areas where it is safer to travel in a group.
Within the city one must take precautions and stay within the known neighborhoods.
Guatemala, just to the West, is a four-hour bus ride, and travel to Guatemala City on holidays and vacations is fairly easy.
The bus service to Guatemala is safe, on time, and reasonable.
Again, if you plan on traveling outside of El Salvador on anything other than official military travel during your stay, it is recommended that you have a civilian/tourist (blue cover) passport. It is recommend that you travel with known personnel, if you're not a fluent spanish speaker, to travel with someone who is well versed in the language.