> Do you have an above average salary for the region you're looking for the apartment in?
Yes, the salary seems to only be part of the issue. Some of the landlords seemed to be slightly offended that a young person makes so much money. Other landlords were searching for long term tenants and did not believe that a young couple was looking to settle down for long enough.
> If so, then who's getting those apartments, if the majority of people cannot afford them?
The supply is super limited. Judging by the rejections I received the landlords are primarily looking for well off young families which the seem to find without a problem. One landlord told me that she received 120 messages within 48h, she basically can choose whoever she wants.
> Is this a special case like SF where there's just not enough apartments being built for the size of population?
This is generally the case all over (west-) Germany. In more rural areas and small towns there is basically no rental market, but purchasing is still unaffordable for most. In my hometown (rural with average income) land prices more than doubled in the last 10 years.
So many young people choose to move to the next city. In my target city, the cheapest apartments I could find for purchase were around 400k€ from 70s to 90s, new construction was usually well above 500k. Rental prices are equally absurd.