Here's a 5+ minute video of "Gridlock Sam" Schwartz about the rise and fall of separated bike lanes in New York City. Schwartz was NYC's tranportation bigwig in the early 1980's. He's for the lanes, but he does a pretty fair job of summarizing almost all of the arguments for and against.
He said that when they put in the barrier lanes, more experienced riders refused to use them. A NYT article I read said that this made the mayor so mad he put up "Use them or Lose them" signs. Also, there were more ped-bike confrontations, caused in part by peds using non-barrier lanes as sidewalks and part by less experienced cyclists enticed onto the street. The confrontations were exacerbated by three ped deaths by cyclists that were not related to the bike lanes. Peds regularly complained to the mayor about cyclists.
The final straw on the camel's back was a comment that an opponent of the mayor made to the President when he was visiting the city. Words to the effect of "See how Mayor Koch is wasting your money."
Edit: I just noticed that there are another 28 minutes of interviews with Schwartz on this topic on YouTube. I haven't watched them, but they are here: