I don't think that "you're welcome" has to be smug or sarcastic, but it does imply a superiority or even equality of status that is questionable in an employee/customer relationship.
I mean, maybe I've got that wrong. Maybe I need to look at this as me helping someone because I do know how to do some things they don't, and it's not a status thing, but just a social specialization thing.
But yeah, a guy just came to get his glasses and he said "thanks" and I said "OK".