I guess I just don't see the logic in the government supporting an airline that is reporting negative profits.
That's because you don't live in a kleptocracy and thus don't understand the nature of one. The government is using taxpayers' money, and the tax burden falls mostly on white people even though there are some amazingly wealthy blacks, to subsidise a non-profitable airline which provides employment and transport for people who support the ANC at a high level. Many of SAA's senior executive positions and prestige overseas postings are held by ANC supporters.