It's odd that the article avoids the question of where crime occurs in the city, as that might provide some answers. A few months ago I made many data visualizations of where criminal arrests occur in San Francisco: http://minimaxir.com/2015/12/sf-arrest-maps/

The tl;dr is that, as expected, SF crime is centralized in the Tenderloin, with 16th St Mission being a close second. However, as the years progressed, crime has become relatively less centralized around those areas. (there wasn't much activity on Lombard Street, though.)