From what I can tell, whenever you hear about "subsidies", as it relates to combustible hydrocarbons, it isn't the kind of free-taxpayer-money boondoggle you see with (for example) a loan guarantee to Solyndra. It usually takes one (or both) of two forms: 1) The tax treatment of any capital-intensive industry, with a tip-of-the-hat to the "how do we account for depleted resources" question (you see the same pondering happening now with bitcoin, for example), and 2) not properly accounting for externalities in taxing the extractor, the oxidizer or the consumer of the point-of-service joule.
In brief, #1 means: "I don't like it, and things I don't like should be taxed more, and until they taxed more, I will call this gift of non-taxation 'a subsidy'"
As for #2, the negative-externality objectionators make a very fair point!