It's my experience that this holds true over more kinds of things than coffee shops. Large chain stores do things even when they're a pain from the employees' perspective, but small, independent shops tend to have the owners as workers in the shop, and so they make decisions which sometimes look like the decisions employees would make, rather than those that maximize profit and goodwill.

I've found this to be so for specific examples of grocery stores, bookstores, coffee shops, and hobby shops, at least. Sometimes the product is enough better to make up for this, though (especially with coffee).