Thanks for all the replies, especially mihlbach. I think you just have to get used to it. I already am, actually. This morning (4th day of riding to work) I was much more inclined to get into traffic, especially when cars are making right turns onto cross streets.

jvossarian, I have taken the Queensboro Bridge route into Manhattan and on paper it seems like a better route, but a) crossing into Queens over the Pulaski Bridge you are supposed to dismount (it's pretty narrow) and b) the exchange and intersection at the bridge is a nightmare. Perhaps with time I'd become more used to it, but it just seems like more trouble than it's worth.