You should note that, despite what many believe, we don't really "subsidize" fossil fuels to any major degree. The majority of the "subsidies" people whine about are just plain old tax deductions - the same ones that other businesses get. The oil companies didn't even get those deductions for a long time, and people complained when they finally got to deduct for exploration and drilling expenses in the same way normal businesses deduct for operations.
There are a few real deductions they get, though - alternative energy research, for example. And, technically, the Strategic Petroleum Reserve counts (although that's just the government buying and storing oil in case of an emergency - and counts for about 2/3 of all actual subsidies). Compared to the size of the industry, it's tiny. Overall, the "subsidies" fossil fuels get don't affect the end-user price much - maybe a half-cent per kilowatt-hour in some markets.
Compare to the various alternative energy sources, which get massive subsidies - and are still three to five times as expensive.