The Bay Citizen did an analysis of all 1700 of the recorded complaints about taxis in San Francisco. Complaints were sent to the city's 311 compliant line. The 1700 complaints span from July 1, 2011 to June 30, 2012 and represent a 13% increase over the previous time period.
The complaint list is an interesting read.
SFMTA has one person in charge of investigating complaints.
Poor quality taxi service is one of the reasons why users seem to be so enthusiastic about new ride-sharing services Sidecar and Lyft as well as taxi-replacement service Uber. Payment and overcharging are not a problem as all of these services handle it directly via a smartphone app. Users can complain directly to the company if they have any issues. Lyft, Sidecar and Uber have a lot of incentive to take complaints seriously as users won't continue to patronize them if drivers are rude, refuse to take them places or drive in an unsafe way. Because trips on these services are booked via smartphone, every trip is tracked so a user has a record of who the driver was, whereas with a taxi and a cash payment unless you remember the can drivers ID you may not know who to complain about.