Almost by definition, our young libertarian's job is to celebrate the profit motive from the offices of a not-for-profit organization. He is subsidized, in other words, to hymn the unsubsidized way of life. Rugged individualism may be his creed, but a rugged individual he ain't.
Just as an aside, rugged individualism is not my creed. I call myself a civil societarian (trying to Google the essay where I coined the term, I find that I made wikipedia).
Where Frank is wrong is in putting the moral onus on those who are subsidized rather than the subsidizers. In fact, I would argue that there is nothing morally wrong with receiving a subsidy, even from government. The moral corruption in government subsidies is not in the recipients, except insofar as they deliberately pressure legislators for money. The moral corruption is in the subsidizers, who are taking money involuntarily from A to give it to B.
With private charity, funds are collected voluntarily. In civil society, I see the subsidizers as inherently less corrupt, because they are not using the power of the state to fund the subsidy. Still, anyone involved in charity has an obligation to ask whether the funds are being used for good purposes.
For libertarian foundations and the like, it is the subsidizers who should constantly be questioning the worth of what they are doing. One question to ask is whether it is more valuable to preach against the state or to compete with it. Should the marginal dollar go to support a libertarian scholar or toward a private school scholarship fund?
For individuals, I offer the same advice that I give to my daughters, which is to heed the market. Market signals tell you where you are most valuable. The highest-paying job is likely to be the job where you contribute most to general welfare. Having said that, you are certainly encouraged to take other quality-of-life considerations into account. Location matters (cue Richard Florida). So does the set of people you interact with on a day-to-day basis. You should learn from your colleagues. Interpersonal stresses are inevitable, but break away from situations where they become overwhelming.
Generally speaking, it's morally safer to work for money than to work for a cause. People who are fanatical about causes do much more damage.