According to the USGS, "Each year the southern California area has about 10,000 earthquakes. Most of them are so small that they are not felt. Only several hundred are greater than magnitude 3.0, and only about 15-20 are greater than magnitude 4.0. " Although San Francisco is not exactly southern California, the general idea is the same. There are many microquakes each day, but this morning's quake was an unusual one. (In fact, according to the USGS site right now, in the 12.5 hours since this morning's quake, there already have been 11 more earthquakes in California today!)
Earthquakes, as most of you know, are a consequence of moving tectonic plates and are measured using the Richter scale.
The Richter scale is a standard scale used to compare earthquakes. It is a logarithmic scale, meaning that the numbers on the scale measure factors of 10. So, for example, an earthquake that measures 4.0 on the Richter scale is 10 times larger than one that measures 3.0. On the Richter scale, anything below 2.0 is undetectable to a normal person and is called a microquake. Microquakes occur constantly. Moderate earthquakes measure less than 6.0 or so on the Richter scale. Earthquakes measuring more than 6.0 can cause significant damage. The maximum quake rating ever measured is about 8.9. - HowStuffWorks
(image borrowed from some guy's blog)