Yes and no. There's a tremendous overhead cost that comes with those companies, but a lot of it has to do with NASA reporting requirements. There are some fairly serious problems at the systems engineering and management levels, too -- an over-reliance on process, as a replacement for knowledge, which leads to bloat in non-productive staffing.
However, the business itself is intrinsically expensive: it takes thousands of people to keep the Shuttle program going, even when it's not flying. There's nothing you can do about that.
Why don't they give Dick Ruttan and his company a shot at designing the replacement space vehicle? NASA needs new blood and innovative thinking, NOT the means of throwing more money at the same old problems.
Because, quite frankly, Rutan has no idea what's involved once you get below the top-level stuff. They'd have to re-learn old solutions. You labor under the misperception that the current crop of engineers and scientists are stupid, and that Rutan has some sort of magic wand. Sorry, that's just you responding to Rutan's smoke-and-mirrors pitch.