As a practicing CPA and a one time mineral exploration geologist, I see lots of debates concerning Federal subsidies, particularly concerning the oil and gas business. What I see most often is a misuse of the term "subsidy". Most debaters refer to the O&G business as recipients of "billions of dollars of subsidies" when in fact they are referring to the fact that O&G businesses claim billions of dollars in deductions for the expenses incurred in the exploration for, production of, and refining of their products. To the greatest extent, these deductions are ordinary in every sense--just like my little CPA firm deducts office rent, payroll, payroll taxes, housekeeping services for cleaning the office, and the costs of our computers and software, and just like my plumbing contractor client deducts his payroll, tools, vehicles, and office rent on his sole proprietorship Schedule C. Our deductions are not subsidies in any sense, and I would argue that O&G companies also benefit primarily from simple deductions rather than subsidies.
By contrast, the $7,500 tax credit for purchasing hybrid automobiles, the 30% of cost tax credit for purchasing home solar equipment, and the loan guarantees obtained by companies like Solyndra are actually subsidies--they are direct payments by the government to purchasers of certain favored products which is a clear inducement for consumers to purchase the products, and the loan guarantees are the principal manners by which otherwise shaky industries which are poor credit risks can obtain credit in the regular capital markets, so when the guarantees are paid, they're subsidies, too.
I've opined for much of my 36 years in practice that large scale tax code simplification will never happen for one principal reason: As important as the Code is in terms of collecting revenue, it provides an equally important power for the government to exercise economic and social engineering. I can't envision either the Federal or state government giving up that power.
So, in discussions about the various merits and demerits of developing technologies, it's helpful to properly distinguish between real subsidies and simple tax deductions for ordinary and necessary business expenses. All businesses get the latter, and the chosen few get the former.
Foy