The main cause is pretty simple. The police in San Francisco just do not bother them in certain neighborhoods. In most other cities police routinely pick up the homeless and dump them some place far.

So the absence of homeless is usually not a sign of better humanity, it is usually a sign of cruelty. This is especially the case in the US. There are other countries where they have better treatment for poverty and mental illness (most homeless are mentally ill to some extent) where the absence of homeless on the city streets may mean actual absence of homeless. But this is not the case in the US.

Thus, even if the sight of homeless in San Francisco is so terrible, one should keep in mind that San Francisco provides the best treatment for them in America.