The research I've read recently indicates (responsibly) running red lights and stop signs decreases a cyclist's chance of getting hit. When stopped, a cyclist is less visible and mobile. Vehicles can be less likely to see them, and they're less able to maneuver out of dangerous situations.

http://www.chicagotribune.com/news/local/breaking/ct-bike-st... (I've seen other sources, but this is the first one I found first just now)