Taking a persons money and not fair at all

Will never ever take first flight with flysafair. OR Tambo boarding gate full waited in line and to find out I missed my flight but because Im late but the airplane was still there 5:43 at C11 . Booked and payed a new flight people got on the second flight 7:27 and the time was 7:30. The lady who assisted me at the counter was sooo rude telling me im not paying an new ticket only the difference not true its a new ticket do I question her about everything she do and that se don't know her work, she then told me I can be on standby if someone is late. Its not making any sense Safair is taking peoples money because first flight and second flight does not have the same rules with flight times. They didn't call me one's