Leaving on a jet plane...Hopefully with luggage!

We had a 5:30am wakeup call in order to drive from Franschhoek to Cape Town airport. We fly from here to Johannesburg...switch airlines and then on to Nairobi. It was and still is a little concerning when the South African Airlines ticket agent told us that he wished we had enough time in Jo'burg to collector luggage and rechceck it ourselves. Our layover is not long enough he said! He explained that he had checked it on to Nairobi, but it would have been "safer" to collect and recheck. Safer because why??? It might not make it to Nairobi or because it will be broken into even though is it locked? He shrugged his shoulders as if to say...BOTH!!!! UGH!!!!