I ride my bike to and from work pretty much every day in SF, and I readily admit that adding these markers most definitely does interrupt and disrupt traffic flow.
The fact of the matter is, sometimes delivery vehicles and service vehicles need to stop and block traffic. They tend to pull over as far as possible to the right, so as not to impede auto traffic. Often this means pulling over into the bike lane. (Note that when there is no bike lane, these vehicles block the right-most lane of auto traffic and cars just go around without getting too hot and bothered. But I digress.)
Erecting the markers prevents this behavior in many instances. You can decide to be in favor of the new bike lane markers, but you can't pretend that the added markers aren't a unilateral alteration to traffic flow that does have an effect.