It's a combination of things. Justin Smith getting hurt and becoming ineffective meant little to no pressure on the QB, and given enough time any QB will torch a secondary.
That doesn't mean that there aren't issues with the secondary though. Both Goldson and Whitner are hit first, cover second guys. There needs to be a guy that attacks the ball and not just tries to decleat people.
Yes, but even if you look at last year when Smith was healthy, the Niners could still not stop anybody's passing game. They were absolutely shredded by the Saints, and New York Football Giants' WR Cruz ripped'em in the next game.
Niners would have a lot less drama if they could improve the secondary, it's their only glaring weakness that will hopefully be improved in the offseason. Draft is only 2 months away!

Surprised it took you that long to start it again 