Oakland is HUGE. You can't generalize it that much. There are so many sub area in Oakland that range from insanely dangerous and crappy all the way up to incredibly safe and beautiful (Rockridge, Piedmont). Also areas near Oakland like Emeryville are getting much nicer.
Unfortunately the prices in these places are also skyrocketing. I started paying $3k/mo for 1400sqft in a not great part of Emeryville last year. The current price for my exact same unit is $3400.
the East Bay is way bigger than Oakland/Berkeley. Walnut Creek, Pleasant Hill, the Lamorinda area, Danville, Pleasanton -- all very nice, safe towns with good bart access. No startups there though.
That's the point - you don't have to live in SF or rent office space in SF, you can avoid SF altogether while still having the benefits of the startup scene an hour away.
Doesn't mean there aren't real disadvantages, but it's something most people/startups should at least consider.