I'm not sure that I would go as far as Tim in calling academic critics of Minerva "foolish"; there are some good reasons for social scientists to be wary of close collusion with the military apparatus of the US government. It's true enough that academics will be designing their own projects, but the availability of new sources of money has a strong influence on how academics behave and we're likely to see more projects that have, as a secondary goal, the furtherance of US military hegemony.
Moreover, the implication that research might become more difficult and interview subjects more reticent because academic departments and disciplines have close ties with the Pentagon is hardly silly; I suspect that, even if a particular scholar doesn't take Minerva money, it would be harder for her to get data in China if her departmental colleagues took the money. Finally, there's the enduring notion that social science should be about, well, science, and not about the pursuit of US foreign and military policy.
That said, I have no personal objection to the program, and would not be reticent about applying for the money myself. But I nevertheless recognize that social scientists have good cause for wariness; the work of social scientists has, in the past, been put to ill use by governments, and distancing the disciplines from the state has some appeal.
--Robert Farley