One reason I think people are so resistant to this idea is because it challenges their assumptions about the division between body and mind*** when it comes to health. By focusing solely on the physical body as the source of all illness and thus healing, modern western medicine has rejected the power of the mind to heal OR be the source of illness. Paradoxically, I think this focus has benefitted individuals who suffer from mental illnesses like depression. But I think if Begley is right, and most anti-depressants work in a placebo manner, we should really re-think our assumptions about the mind's role in our physical illnesses.
When a patient presents with symptoms of heart disease, a doctor naturally attempts to treat the heart. This is because heart disease is an umbrella term for a whole host of problems associated with the heart. Since we are currently ignorant of the precise physical manifestations that cause depression, its more properly described as a disease of the way a person is thinking or feeling that causes them to feel predominately sad, empty, lethargic, lonely, apathetic, etc. So, naturally, when someone presents with depressed symptoms, the doctor wishes to treat the person's thoughts and feelings. Anti-depressants do exactly this. They give a person a tangible way to think and feel healthier about their depression. First, they physicalizes the symptoms of the illness, separating the individual from their depressed symptoms. Like a bad case of the measles, or even a cancer, depression becomes something that can be fought with physical manifestations like medicine. Further, they remind individuals that they are not alone in their sadness, that there is hope for them, and that they are doing something productive to help their problem. And for 75% of people, this treatment, this physicalization of their thoughts and feelings really helps them, and they are able to improve their depression.
This description does not deny that depression is caused by something physical within our brains--far from it. What I'm suggesting is it's precisely because we emphasize depression's physical dimension, and probably treat it in some way that we are unaware of currently that we give individuals a better chance at defeating its mental symptoms. But, if we admit this to be the case, then it becomes a lot more difficult for us to deny the converse of this conclusion: that if we emphasized heart disease's mental dimension we would give people a better chance at defeating its physical symptoms. I don't know for certain whether this would help people or not, simply because the research hasn't been done--(and it's debatable whether scientific research could be done, since the hypothesis seems to be questioning the scientific method). But I do think that these are assumptions that are implicit in our modern understanding of depression are the reason why Begley's article caused so much controversy. And yet, the facts remain that these drugs have helped a lot of people feel a lot better (to table the issue of over-prescription, which I think is valid). So, I think the public revelation that anti-depressants are primarily placebos should be taken as a general wake-up call for our one-dimensional view of illness in general.
***Caveat here: I'm not trying to argue here for a dualist view. When I make the distinction between mind/body, I mean to the extent that anyone distinguishes between mental/physical illnesses: that there is physical cause for the mental ailments, but the causes are so far from our current neurological understanding that the distinction still makes practical sense.