Alex, your central point is well taken, and too often overlooked: In relation to energy delivered or sales, fossil fuels get far less subsidies than renewables and other alternatives do.
I have one quibble though re: "Often, a choice to end a fuel subsidy is a choice to make energy more expensive for the poorest among us." Most economists agree that subsidizing consumer prices is counterproductive. Here is what a literature review by IMF economists concluded:
This paper reviews evidence on the impact of fuel subsidy reform on household welfare in developing countries. On average, the burden of subsidy reform is neutrally distributed across income groups; a $0.25 decrease in the per liter subsidy results in a 6 percent decrease in income for all groups. More than half of this impact arises from the indirect impact on prices of other goods and services consumed by households. Fuel subsidies are a costly approach to protecting the poor due to substantial benefit leakage to higher income groups. In absolute terms, the top income quintile captures six times more in subsidies than the bottom. Issues that need to be addressed when undertaking subsidy reform are also discussed, including the need for a new approach to fuel pricing in many countries.
Essentially, fuel subsidies don't really make energy less expensive for the poor. At least, they don't make living less expensive. The cost of the subsidy is just shifted. The overall effect is to weaken the country's finances, and ultimately make everyone poorer.
Moreover,collateral effects of fuel subsidies may be even more damaging. In India, for instance, most vehicles use diesel fuel because of heavy government subsidies. The mass of mostly dirty diesel engines spews a toxic smog that has caused an epidemic of cancer an other illnesses, as Businessweek has reported. Sickness, health care, and pollution controls impose other costs on the poor that offset -- maybe more than offset -- any economic benefits from fuel subsidies.
Note that government subsidies for renewable or nuclear energy bring their own set of unintended, often negative consequences; such problems are not limited to fossil fuel subsidies.