A counter is a surface used for making transactions in a store or in a home kitchen for preparing food. In a store, you pay for items at the counter.
When counter is a verb, it means "to speak up in opposition," like when you counter your opponent's argument in a debate. When something conflicts, you can say it "runs counter to," like a fancy car that runs counter to your philosophy of living simply. You can think of this meaning as "in the opposite direction," like "counter-clockwise," meaning the direction that's opposite of clockwise.