Notwithstanding the advent of 'suicide passengers', my take on it is slightly different. As I see it the theory behind unaccompanied bags not travelling without owner is, in the good ol days, all but the nuttiest bad guys generally wanted to live. This meant that they preferred to not be on the targetted aircraft, and keeping people with their bags was a simple deterrent. Unfortunately, now martyrdom has become far more fashionable, whether the passenger travels onboard or not has become far more academic.
That said, there is undoubtedly a difference between a planned separation of pax and bag, where pax doesn't show at the gate, and an unforeseen one, where a potential terrorist couldn't have known his bag was going to travel separately, and as usual it comes down to levels of risk versus complete chaos if all rules were rigidly applied.
Air Nova (a feeder of Air Canada, if they're still in business) used to routinely separate pax from bag if the aircraft didn't trim - which was about 50% of their trips - although this was pre-9/11.