Doing research for a company has the end goal of benefitting that companies' shareholders. Doing research for a publicly funded institution has the end goal of benefitting society.
Look at the decoding of the human genome. No company has a patent on that because public institutions did it first.
While patents on genetic sequences have some tricky specifications (you have to patent "non-standard" biological uses), I know Celera holds a number of patents related to the Human Genome Project. From what I recall in general biology, Celera actually used automation to outpace the public institutions even though they started later.
If you're curious, here's a patent list and some background on the company:
Arguably, though, goals and results are two different things. "The road to hell is paved with good intentions", and all that. What does the evidence say about which benefits society more?
A company works for its shareholders, which are a very restricted group, and public funds work for society. Intuitively, the outcome is clear. It's also supported by actual data: wages stopped rising in the US in the 1970s, while productivity kept going up; this is correlated with the introduction of concepts like "shareholder value".
To add to the above: Pretty much all companies benefit society; it's hard to think of counter-examples.
Sure, oil companies spill oil sometimes; but they (should) have to pay for that.
Big telcos tend to have monopoly status, and exploit consumers, but they do that not because they are companies, but because they are in a patron-client relationship with the government.
Some companies produce tremendous benefit to society; others produce small benefits, which matter a lot in the aggregate.
Taxation is not theft. It is a societal agreement. I know of no society, except extremely primitive hunter-gatherer societies, that has no notion of tax for public services.
And even there, you could say everyone is "stealing" from the public goods all the time. (if you hunt and eat an animal, then you have stolen it from the rest of the people).
When did I agree? Do I have a choice in the matter? How does one opt out? It doesn't sound like any kind of agreement I have ever heard of.
What is a public good? Who decides what is public?
If I hunt and eat an wild animal, i.e. one that was not raised on a farm, I am not stealing it from anyone. By your definition the only way I am not stealing it is if I kill it and divide equally to everyone.
This choice is decided in a democratic process. Countries with very high levels of taxation and public services (e.g. scandinavian countries) have earned a high level of trust from their voters that the money is put to good use.
To pay less taxes you could either relocate to some place with less taxes (this is quite possible in the US, since state and city taxes vary). Or you could work democratically to change the system. If you really want to live in any place approximating anarcho-capitalism, you would have to move to a 3rd world country.
If one could opt out of taxes, that would be the end of the tax system. Of course no individual wants to pay for the public services. Everybody want the other guy to pay! In the same manner, you could ask why one cannot opt out of the penal system.
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As to the "hunting as theft" issue: as long as there are plenty of animals to hunt, you are not taking from anyone. That was the state of affairs 100,000 years ago. When resources are limited they must be managed/taxed in some way. Humanity has not solved most of these issues at this point. See also: http://en.wikipedia.org/wiki/Tragedy_of_the_commons
So you could ask: when did I agree to those japanese fishing vessels depleting the fisheries next to my shores, do I have a choice in the matter? Their fishing raises the price of wild fish and serves as a de-facto sushi tax, only you don't get to eat any of the sushi...
My point is, we are not in the paleolithic period anymore. The world is too complex and resources are too few for fully individualistic economic philosophies.
That's strange. If you do your job properly, why shouldn't you get paid even if it is by the taxpayer?