One of the things you quickly learn when delving into any area of science is that there are tons of published articles coming down on either side of an issue. This was pretty shocking to me as I was completing my PhD, I went in with the naive idea that science was cut and dry. It is not. You learn that you need to consume as much as possible, critically evaluate everything, and then weigh the balance of the evidence.
That is what organizations like CDC or HHS do. They have scientific comittees dedicated to hunting up every bit of published research. They read it all. And based upon that, they decide which policies are in the best interest of public health. Neither you or I have the time available to aggregate and consume all of that information, which is why we need to rely upon these organizations.
They don't always get it right, and sometimes their recommendations change time over as research/evidence changes. These committees are especially slow to backtrack if new evidence contradicts their prior recommendations. There are also political influences. But the process overall is sound, if not nimble.
If you want to read some contrary evidence to what you have posted, here is a peer-reviewed article estimating that
influenza vaccinations in the US prevented 40,000 deaths from the '05/'06 flu season through '13/'14. Almost 90% of those prevented deaths were in individuals 65+ years of age. Here is another article estimating
similar vaccine effectiveness in younger and older adults (for both groups, effectivness values ranged from around 10%-60%, depending on the viral strain).
On a side note, there is cool work being done towards a universal influenza vaccination that could prevent all varities of influenza, as well as novel anti-viral therapies in the treatment of flu. Hopefully progress will be made in those areas.