Interesting question. I think, for Cape Town's MyCiti anyway, the large cost was for totally new infrastructure - stations, dedicated lanes and, of course, brand new (Brazilian) buses with their touch-'n-go card pay systems. MyCiti is based on cities like Curitiba, except those examples could not easily be applied to SA's apartheid-era spatially inefficient, decentralised urban planning, which added to MyCiti's cost (long distances). 
The selling point for these systems is they're 'rapid' - buses in dedicated lanes are not going to get stuck in traffic like other motorists, so people would want to use them, and it's cheaper than private car (fuel, wear & tear, long travelling times on congested roads).  Note other cities w/ functioning, efficient mass bus systems like London and Rome don't use dedicated lanes except here and there. So there's your billions, not overpriced tenders.
BTW Cape Town has increased street 2017 parking rates by almost 60% to about R17/hr, above private rates!