In my opinion isolating separate transportation modes is only good if it is complete isolation but that's never feasible in a city. Too expensive and space-inefficient to make every intersection collision-free for cars, bikes and pedestrians.
If you separate cars, bikes and pedestrians most of the time but their paths cross at intersections then you have a problem because drivers might not expect a sudden bike lane out of nowhere. It's better to have the bike lane on the street so that cars see it all the time. This makes them drive slower and more carefully because they expect bikes to show up there.
I don't have data to back this up although I vaguely remember reading about it in "Streetfight" by Janette Sadik-Khan. If I recall correctly introduction of unseparated bike lanes in New York City didn't increase bike fatalities despite increasing the number of bikers and it also decreased number of pedestrian fatalities thanks to cars driving slower because of bikes. Of course the article shows that now the pedestrian deaths increased so it might have been a premature conclusion on Sadik-Khans part.