I found a great article on Slate about the "controversy" that we all face every year: a flu vaccine.
I personally don't think it is a controversy, as data is pretty much in, and, with some necessary uncertainty found in any scientific problem, we know that generally flu shots are good for the general population as a whole.
In the end, it’s easy to ascribe sinister motives to flu control efforts, especially if you’re unwilling to tolerate uncertainty. With a slight shift in perspective, however, one can see our evolving flu control programs as a triumph of public health.The article is a good read and it presents this complex issue rather clearly:
The Flu Vaccine Controversy