With a population of 805, 235 in 2010, San Franciso was one of the largest cities in California, with it being the fourth largest city in the state.
By the time of The Walking Dead, just like Los Angeles, San Francisco was engulfed in chaos and destruction during the outbreak. becoming overrun by the dead. However, the military was initially able to close off the marina to all boat craft. But soon, San Francisco was declared overrun and as a result, completely burnt down, in accordance with the regulations of Operation Cobalt. Some survivors managed to escape San Francisco, considering Travis' group stumbled upon the remains of a destroyed boat with logs stating the city of San Diego was completely burnt.
The ship log that Nick picked up from the overturned ship reveals that San Francisco has been destroyed by the military.