Because the nature of the two programs was fundamentally different. The Shuttle was a product contract, while CCP is a service contract. On the former, the govt has much more control, and will detail more rigorous acceptance criteria. This generally gives a much higher pedigree on quality control. On the latter, they take a much more hands off approach and have limited insight.
As an analogy, imagine you are making a big bet on acquiring a software company. One company gives you their source code, shows you all their most recent static analysis, unit test results, allows you to interview their programmers etc. The other company allows you none of that, but gives you a chance to play around on their website to see for yourself. Both systems seem to work when you try the end product, but which do you have higher confidence in?
At the end of the day, "reliability" is just a measure of how much confidence we have that a product will do what we ask of it, when we ask.