All people who pull into the "search your car" lane set up by the CA Highway Patrol get across the bridge without paying the $2 toll. Search is required of all who fit the "profile".
Also, don't you think that the most effective way to accomplish this bombing is to put several cars in convoy, each with a trunk full of fertilizer bomb? Vans and trucks will obviously be the first to be searched if this threat becomes credible, so I would expect the terrorists to consider alternate methods.
Anyway, I say mount a few .50's on the bridge approaches and maybe several 25 mm cannons here and there. Along the coast on both sides of the bridge there are quite a few old bunkers and gun implacements left over from WWII; I think they would still be useful for protection of the bridge and San Francisco, if the latter is still worth protecting.