While the extra money will go to retrofitting, the new snazzy Bay Bridge suspension bridge redesign is what triggered the increase in the first place -- you may recall that when Schwarzenegger tried to scrap the $2 billion original plan for a big slab of concrete, we only managed to save the design by getting a lower bid ($1.4 billion) and by agreeing to raise tolls on all the area bridges too. (For what it's worth, the Bay Area Toll Authority claims we would've gotten a $4 increase no matter which bridge design was picked, which we actually believe.) Plus -- it could always be worse: you could drive in New York ($9 on the Verrazano Narrows, $6 on the GW) or Virginia (the Chesapeake Bay Bridge is $17/$24).
As SFist Jon's already noted, your fare'll stay the same this month if you've got a FasTrak, but will go up to $4 as of Feb. 1. As an additional bonus, there will also be more FasTrak-only lanes put in. However, on the down side, it's still pretty difficult to get a FasTrak, as the negotiations to sell them at Safeway and Costco seem to have stalled.