It makes sense considering the 49ers came to CA from all over the country during the Gold Rush and many stayed (John Sutter of Sutter's Fort was German Swiss). Also, quite a few soldiers of German descent were likely stationed at the Presidio and then settled down in the area when their service was done. My German grandfather did that after the War of the Phillipines in 1900 and actually brought much of his family out from the Midwest. They were there during the 1906 quake. Keep in mind that at that time Germans comprised the largest ethnic group in the U.S. so I'm sure they were just about everywhere. Here's probably the most famous one who immigrated then:
http://en.wikipedia.org/wiki/Levi_Strauss
Here are a couple of places that would have more info on SF history if you're in the area:
http://www.californiapioneers.org/visitor_info.html
http://bancroft.berkeley.edu/