Jackson's findings showed that outside of flu season, the baseline risk of death among people who did not get vaccinated was approximately 60 percent higher than among those who did, lending support to the hypothesis that on average, healthy people chose to get the vaccine, while the "frail elderly" didn't or couldn't. In fact, the healthy-user effect explained the entire benefit that other researchers were attributing to flu vaccine, suggesting that the vaccine itself might not reduce mortality at all.
That quote is from this Atlantic article, which has a good analysis of the (rather sparse) medical evidence behind vaccines. It includes the following paragraph:
The annals of medicine are littered with treatments and tests that became medical doctrine on the slimmest of evidence, and were then declared sacrosanct and beyond scientific investigation. In the 1980s and '90s, for example, cancer specialists were convinced that high-dose chemotherapy followed by a bone-marrow transplant was the best hope for women with advanced breast cancer, and many refused to enroll their patients in randomized clinical trials that were designed to test transplants against the standard—and far less toxic—therapy. The trials, they said, were unethical, because they knew transplants worked. When the studies were concluded, in 1999 and 2000, it turned out that bone-marrow transplants were killing patients. Another recent example involves drugs related to the analgesic lidocaine. In the 1970s, doctors noticed that the drugs seemed to make the heart beat rhythmically, and they began prescribing them to patients suffering from irregular heartbeats, assuming that restoring a proper rhythm would reduce the patient's risk of dying. Prominent cardiologists for years opposed clinical trials of the drugs, saying it would be medical malpractice to withhold them from patients in a control group. The drugs were widely used for two decades, until a government-sponsored study showed in 1989 that patients who were prescribed the medicine were three and a half times as likely to die as those given a placebo.
I've known for some time that doctors are not scientists. They generally know nothing about the scientific method: testing theories against evidence. Their actions have almost nothing to do with data, or statistics, or how to truly uncover truth. They simply guess, and then claim that their guesses are beyond questioning. Studies have shown that the treatments doctors prescribe are based not on evidence, but on what other doctors around them are doing.
The only thing you can say in their defense is that all of the 'alternative medicine' out there is even worse. What is it about medical care that makes people act so irrationally?
I found Jackson's vaccine study via Google Scholar, and read it. It looks like a good piece of science, but there are a few things in there I do not know how to interpret properly. I've asked one of the professors in our departments, a statistics expert, for his opinion on the article. Unless he finds a serious problem in the study, it is probably safe to say that flu vaccines really don't do much to prevent mortality in people older than 65.
Note that the study only looked at death rates in old people. It may still be true that vaccinating young people, who are most likely to spread the flu and have a stronger reaction to the vaccine, would prevent overall mortality. I have seen many scientists write that our current vaccination strategy is flawed, and that we should focus mainly on the people who might spread it.