For our internal flights between Cape Town and Johannesberg, we have been reserving on Mango Airlines. They have a mandatory "green fee" (not much, so hard to complain), and then there is the option of taking your bike on the plane for an extra $25.
The web site operates bizarrely. Unlike American airlines, where the low prices are available early on, then steadily go up, lower fares appear pretty much at random, so if you don't like the fare you see one day, hold on and try the next and it may well go down. In the end, we can fly 4 people roundtrip between Johannesberg and Cape Town for $520 or $605 depending whether we are following the Group C winner or the Group C runner-up. Not bad for such a long flight (800 miles).