I think the reason that the FALA-FACT never seem to work is purely because of the cost to pax.
Think about it... In the mornings when Link went out of Lanseria you could get a ticket for probably R1500 or so? But very close to that exact time there is about 4 or 5 other flights going out of Jo'burg for half that price.
I think saving R700 is definitely worth the extra trouble of going trough Jo'burg.
My personnal opinion is that a "low cost" airline such as Kulula or One time would make a killing on that route. Link plainly can't offer the prices that they do.