As I said in this case there was no bike lane and my understanding is that this is a known danger and the cyclist should not have been passing all the stopped cars on the right. See example #8 on this page: http://bicyclesafe.com/
The disadvantage with going into the lane is that cars have much shorter stopping distances. I had an accident a few months ago where I had just managed to merge into the lane (had to be going at the speed of traffic to do this) when all the cars in front of me slammed on their brakes and skidded to a halt -- I hit the back of the car with my head and smashed my helmet (and got cuts in my head where the helmet cracked; but I'd have been severely worse off without it!).
But right hooks are much more common than what happened to me. We just have a really bad road infrastructure in the US (even for driving -- I'm amazed every time I go back to the UK and can drive for miles through densely populated areas without stopping, all because of the roundabout -- the lockless n-way intersection).
As you imply, "separated" bike lanes are another matter. It's as if one is on a pleasant jaunt through bucolic parkland, punctuated repeatedly by intersections with angry vehicular traffic that can't possibly see the cyclist before she enters the intersection. It's probably possible to design these so that don't have problems at every intersection, but the concept in general doesn't lend itself to that. My suspicion is that separated lanes are an attempt to turn cyclists into pedestrians: stop at every intersection, never enter the street, stay the !#@% out of the way of red-blooded American car drivers. No thanks! When I want to travel as slow as a pedestrian (and in many cases I do) I just leave the bike at home.
Bikers on public roads should also be licensed and insured just like car drivers. Equal rights, equal responsibilities.