A few things:
Cancer is basically the most likely thing to kill you besides heart disease. A physically active population will have less death by heart disease and thus more by cancer (because something has to kill you). So perhaps there's just less heart disease in SF.
They say things like "rates are soaring" without saying how much and if it's different than national averages.
This article has very little substance and is basically stating the fact that a lot of people get cancer. IIRC, any given person today has a 25% chance of getting cancer in their lifetime.
So don't worry: if you exercise and eat right, cancer will eventually get you wherever you live.
(I should acknowledge the obvious of some environments are literally carcinogenic, so if you live in a coal mine, 19th century London, or modern Beijing, there's more cause for concern)
For anyone looking to learn more about cancer and its history, the book The Emperor of All Maladies is very good.