Beans are a cheap commodity, so to count them is a rather silly thing to do. A "bean counter" is one who nitpicks over small things in order to save costs. It is a derogatory term for accountants, bankers, and anyone who holds a financial interest in an endeavor.

slang derrogatory term used in referring to accountants.

Someone who is in upper management, typically a chairman or CEO of a large corporation, who only cares about cutting costs and pleasing investors.

a banker or accountant

The new employee down at your local Chipotle, that is single handedly trying to save the business by giving you tiny ass portions.

One who accounts for the residents of a Hispanic neighborhood.