The article certainly mentions the holistic view here:
"Taken together, the study shows a statistically insignificant increase of injuries by 5%."
Time's source is the Tribune:
http://www.chicagotribune.com/news/watchdog/redlight/ct-red-...
Emanuel has credited the cameras for a 47 percent reduction in dangerous right-angle, or "T-bone," crashes. But the Tribune study, which accounted for declining accident rates in recent years as well as other confounding factors, found cameras reduced right-angle crashes that caused injuries by just 15 percent.
At the same time, the study calculated a corresponding 22 percent increase in rear-end crashes that caused injuries, illustrating a trade-off between the cameras' costs and benefits.
The researchers also determined there is no safety benefit from cameras installed at intersections where there have been few crashes with injuries. Such accidents actually increased at those intersections after cameras went in, the study found, though the small number of crashes makes it difficult to determine whether the cameras were to blame.
>They also failed to mention that red light cameras reduce the number of pedestrian and bicycle collisions.
From what I can tell, no one has done a study on that and it sounds questionable to me to see any results there. In fact, Chicago has a big problem with cyclists hitting pedestrians since it added so many bike lanes. But that's a discussion for another time I suppose and a problem that'll probably take care of itself as cyclists and pedestrians get used to each other.