I haven't read this about Starbucks in particular, but that is a pretty common trade-off for large retail businesses to make. They accept the fact that a certain percentage of stores will operate at a loss, but keep them in existence for other reasons (branding, in most cases) if the losses can be managed.

A friend of mine is a middle manager at a retail kitchen goods chain you've probably heard of. I've heard from him that many of their stores are always struggling to break even, and that most of the business is supported by a small number of stores that do an outsized amount of business.