It makes the upfront cost higher but if you exchange a used bottle for a new one each time you buy milk it ends up being about the same cost as a plastic jug with quite a bit less waste.
Haven't seen an analysis on the carbon cost of carrying the extra weight, but I would guess it's lower than manufacturing?
I would love to see SF (or anywhere) implement a system for reusable food takeout containers that made it easy for both restaurants and their customers. All you'd need is a citywide standard set of containers. Restaurants get daily container deliveries (only the kind they want) and customers get weekly (or monthly) container pickup. It would probably make sense for Recology (the recycling company) to handle the pickups.