Actually, chemistry and physics do quite well with nonprofit publishers. Compare the profit margins of for-profit publishers with non-profit ones like the American Chemical Society. In 2015, the ACS made a $10m profit on $500m gross revenue, a much smaller profit margin.

http://www.acs.org/content/acs/en/about/aboutacs/financial.h...

The smaller American Physical Society made <$100,000 on $53.5m gross revenue in 2015:

http://www.aps.org/about/governance/annual-reports/

So yes, it is possible to have high quality publications produced on much smaller margins. The question is whether it is possible to provide similar services for similar margins in a for-profit context. Given that for-profit companies, by definition, seek to extract the highest possible profits on what they do, one should really question whether it makes any sense for for-profit publishers to have the stranglehold they have on academic intellectual property.

Why does the logic of "taxpayer funded research should be free" suddenly change when the publisher is a non profit? If that logic is valid, why is the $500 million fine?

I should probably have said "similar charges" as I said later. Reducing the margins to nothing can at best reduce the cost by 30% or so, which I doubt would satisfy most open access advocates; given that, the real concern has nothing to do with publishers' profit.