Ridiculous penalty fee equivalent to flight ticket

Penalty for being late for the flight equivalent to ticket. I was 30 minutes late for my flight and yes it was my fault. But how can the penalty fee be R1000 when my flight ticket was R1085. Secondly, other airlines do check on you when you delay to check in but this flight failed to do so. Lastly, I tried to check in on line and their online check in was closed and not working. I'm unhappy