I gave the Nature article a brief read. It was typical of similar articles I have read on this matter.
Having worked in the petroleum industry for 15 years, I have not encountered any business programs where governments pay oil companies to drill and operate oil wells. That would be a subsidy.
These thinkers tend to consider externalities, royalty payments, and tax schedules as subsidies. While each of economic parameters is worthy of more public discussion and possible change, they are not a subsidy.
The article also mentions the civil discontent that arises when fuel prices go up--just about anywhere in the world. When the government chooses to subsidize fuel because citizens are upset, is this really the fault of the petroleum industry? Methinks the politicians making this decision are more concerned about maintaining power than what is right for society.
I'm drafting an article called "Fracking for Left-Wing Dummies." Stay tuned.