First off, I take issue with the notion that curing disease is the only goal of the NIH or of academic science. Science actually shows that ~2/3 of human disease is self-inflicted, as the WHO points out: "Seven leading risk factors... account for almost 60% of all ill health in the Region." The NIH, correctly, takes a broad view of applied science: "If you ask me, weapons and global warming are greater health threats than diseases caused by overeating.
While Begley claims disease is "unsexy," the reality is that the NIH pours money into medical school research campuses and every scientist has wet dreams about curing cancer. In fact, the last guy to run the NIH (Elias Zerhouni) was an MD who focused almost solely on translational stuff. Begley's argument boils down to a "lack of cures," but that's a loaded metric. As I've pointed out here before, testing a single cure can cost the same as 1,000 research labs per year. The $50b NIH budget just couldn't accomodate that, although we could fund it if we cut back our military. You want better cures? Pay scientists what they deserve.
From the article, it's clear that Begley (who holds only a B.A. and has never done research) thinks science is simple: find a drug, cure a disease. So she can't understand what's holding up the works. But what we've learned over time is that conventional small molecule therapeutics may not work for chronic disease. On the other hand, stem cell technologies and genomics are showing a lot of promise for curing disease. The system is by no means perfect, but I think in 50 years we will look back and realize that it was working, at least as much as we let it work.