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Taxes on a particular econonomic activity discourage that activity. Usually, that's considered a disadvantage, but if the economic activity has external costs, a tax can be a way of raising the private cost up to the same level as the social cost, and thus moving the activity back toward its optimal level. Conversely, subsidies could be useful if the activity has external benefits. The subsidy would decrease the private cost and bring it into agreement with the social cost, encouraging an efficient increase in the activity. Thus, fishermen would pay a penalty tax to bring the private cost of fishing up to the social cost, and public transportation would be subsidized to bring the cost down and raise ridership toward the optimal level.
Economists have often favored these approaches, because they work more like markets -- we like the carrot better than the stick, as a rule -- but governments have not been very committed to, or successful at, putting them into practice. This is especially true of penalty taxes, which are, after all politically unpopular.
What about the impact on the government deficit? In principle, the penalty taxes might more or less balance out the subsidies -- perhaps even balance out to zero. But it's hard to imagine a government with the self-discipline this would require. Some economists and many citizens would worry that a tax that started out as a way of discouraging inefficient activity would end up as a government cash cow.
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