The shower comparison is not a good one. Almost everyone regularly takes a shower, but only a small percentage of the population regularly cycle. The Treehugger author is comparing raw numbers, not percentages. I don't have the stats on hand but I'd bet that, as a percentage of the population who engages in the respective activities, cyclists are much more likely to get head injuries than folks who take showers.
However, I know of two common arguments against helmets and one prevailing issue that I think all cyclists can agree on. The area of agreement is advocacy for more bike infrastructure so that cyclists are inherently safer. In most jurisdictions cars are legally required to share the road with cyclists, specifically in urban areas and on residential roads. But any cyclist (or motorcyclist, for that matter) can tell you that sharing the road with even the safest drivers can be a harrowing experience.
The first argument against helmets, that BSNYC likes, is that mandatory helmet laws (not helmets themselves) deter new riders from getting on a bike. By extension, if there are fewer cyclists then drivers are less likely to respect them and the roads are less safe. As an example, I recently had a conversation with a friend and recommended a Burley trailer to get him on a bike and his daughter to come with him (she's two). His response? She refuses to keep a helmet on, so it isn't worth the effort and he doesn't own a bike.
The second argument is more difficult to prove and I feel like I've read it from BSNYC as well. But, it goes that wearing a helmet makes riders feel safer and therefore they're more likely to take risks, increasing the likelihood that they need the helmet in the first place. I don't know how anyone would ever really prove that, but it was an argument that appealed to me for a while.
I used to wear a helmet when I went on rides for fun or exercise, reasoning that I was going faster and therefore any fall would be worse. But when I commuted in the city I didn't wear a helmet, reasoning that my average speed was slower and I spent a lot more time focusing on not getting killed. Eventually I realized I ride basically the same no matter where I'm going or what bike I'm riding. I don't think I take a huge amount of risk, but I also like to go fast. I ride my class 3 ebike the same way. So these days, I always wear a helmet.