Well that's the gamble you take with young players. They are far more likely to be injured and far more likely to make mistakes, however they are also far more likely to improve massively and eventually become key to winning trophies (than their equivalent 28 year old signing). The problem isn't having Rafael, Smalling & Jones in the squad. All are potentially great player's that have a decent chance of having careers like Vidic and Evra. The problem is a combination of bad luck and that we are trying to integrate too many younger, injury prone players all in similar positions all at once. I think everyone would agree that if Evans had become the defender we all thought we would be (ie not injury prone and very good) 3 years ago we wouldn't have this problem. Evans would be our main defender and one of Smalling, Jones or Rojo would partner him.
The problem is that Evans is nearly 27 and has arguably gotten worse in the last 4 years, certainly in terms of his injuries. I think he is the one that needs replacing most, with an experienced defender with a track record coming in. You have to bear in mind though if you don't want injury prone, error prone player's we may as well shut down the academy and lower our expectations, as buying a £30-50m player in every position isn't a particularly viable business model.
I personally haven't given up on Jones, Smalling & Rafael; as they have all shown enough talent for us to be as patient as possible. That said we obviously need cover, as if we want to have say 8 first team defenders in the squad (Rojo, Shaw, Jones, Evans, Smalling, Rafael, Blackett, McNair) we can't have 4 that are injury prone.