We've had a great number of bike lanes added to many streets here in Jax, Fl and I can say that the author is absolutely wrong about them making car-bike interactions 89% more dangerous.
But then again, I'm just going off the design incorporated into my area; I don't know, but maybe there's something to this claim when it comes to NYC (and other) designs. I don't get them green boxes and would hate to see them incorporated here in my area.
I don't see bikelanes as making cycling safer and I can see how a mindset like that could lead to less safe cycling; bikelanes simply give me more real estate and make it easier for cars to pass, period. I suppose you could argue that for that reason they make cycling more safe, but again, I don't see it that way, because I don't want to become complacent.
As for bike safety/accident studies he cites, I don't trust them, at least here in the states; however, I am curious about the studies he referenced from Europe, since those might be more accurate, but he didn't provide a link...
The article may be more accurate for some areas, but totally off base for my area and experience.