Of course it's a terrible commute, but some people prefer that - it should also be noted that the comment you responded to was talking about the Valley, not SF. Software engineering jobs in SF proper is a raw deal IMO excepting that you get to live in SF & be closer to the offerings of SF (or you can commute into SF, but might as well be commuting to an area with better pay IMO). Engineering quality is probably roughly the same across the Bay Area though.
The average startups are not paying engineers anywhere close to 250k.
But I can assure you that every one of the big 5 tech companies pays those numbers (as do the "hot" unicorns that are on a similar "tier" as Google, ect) .
The moral of the story is, don't work for a startup. Go big or go home. Sell out and work for one of the companies with the actual money.
Because at those companies, those numbers are real.
And the thing that people need to realize is that those "top" companies have a whole lot of people working for them. The numbers don't back up the common argument that is made about how "you have to be in the very top 1 percent of engineers to work at Google, FB, or Amazon".
1: https://www.glassdoor.com/Salaries/san-francisco-software-en...
2: https://www.payscale.com/research/US/Job=Senior_Software_Eng...