Sorry but thats a basic control procedure with any airline as having people pay at checkin disrupts checkin and holds up the line, additionally staff accepting cash at checkin is open for abuse. Standard control procedure with most airlines to protect revenue.
Then only accept credit card transactions at the checking desk... I reckon my eventual card transaction much have taken all of a minute to process - about the same length of time the checkin agent had to spend arguing with me about the need to join another long line in order to pay.