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.

a banker or accountant

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

One who accounts for the residents of a Hispanic neighborhood.