Right, but it was rebuilt in era when humans still knew how to design solid-standing, aesthetically-pleasing buildings for just about any purpose (unlike virtually all of the crap built in the past 60 years). That's why much of its architecture counts as "historic", and preservation-worthy.
Much of the post-fire development used unreinforced masonry and was built on poor-quality fill. We saw the effects of this during the 1989 quake in areas like the Marina district.
The preponderance of fill (and depth to bedrock) in the densest areas of SF is well-illustrated by the Millennium Tower fiasco[0]. The MT's pilings do not even reach bedrock!
Much of the post-fire development used unreinforced masonry and was built on poor-quality fill.
Also, the issue of some buildings being built to (allegedly) inadequate standards is a red herring. If that were the case, the city would be more than happy to have them condemned, and all manner of more useful structures (for affordable housing or otherwise, put in their place).