The median 2 bedroom apartment in SF is currently about $4600/month. This means that even with a roommate to split the bills with, at a salary of $90k you're looking at spending nearly 50% of your take home just on rent. Add in utilities, food, transportation, etc and $90k pretty rapidly stops looking so great.
You could easily live in a 3-bedroom and pay $1700 a month in rent. You'll only have $3000 a month to pay for food and transportation - oh my god, the privation, how is anyone supposed to make it?
"in SF" in a pretty important qualifier. On top of a 28% federal tax rate you're paying 12% state income tax. San Francisco has a 1.5% income tax as well. So on $90k/yr you're down to about $4500 a month take home but that's excluding any payroll taxes outside of income. Several hundred dollars there. You're already in "spend half my check on rent" territory.
Even though 90k is ~3x the average personal income for the US, when you're living in one of the most expensive cities in the country, you can absolutely be broke on that.
SF does not have an income tax. It does have a 1.5% payroll tax that is paid by employers, but that is already factored into your your gross pay (IOW, if a company offers you 90k the pay the $1,350 in taxes and you never deal with it).
You can argue it effectively pushes down the size of the offers people get, but you don't have to worry about it when you calculate your net take home.
You are right, (marginal) state tax on $90k is "only" 9.3% and that's on about 40% of the income.
My point was that on $90k in SF proper, if you want a "nice" place, even a 1BR or studio you're going to be spending a huge percentage of your income on rent and basic necessities.