Really, it's not the same fundamental argument. All you have to do to accelerate in a car is push down a pedal an inch or two. In a bike, it takes longer and more energy, especially if you're going up a hill. Furthermore your awareness and maneuverability are much sharpened while on a bike. And if you hit a pedestrian, you're much less likely to kill him because you don't weigh two tons.
But true, it's safer to stop, and it's the law. As a general rule, I stop for most stop lights, and run most everything else unless it's near a busy road. My dad got caught running a stop sign on his bike a year ago, and had to pay like $140, which seems steep.. hell, before then I didn't even know it was illegal.
Just my $0.02