The NED is not just a "projection" of soft power as Nye defined it. It IS soft power -- the very praxis of it. But so what? The point of Joseph Nye's paper which introduced the term was that soft power is an inherently good thing, and powerful liberal democracies like the US should not neglect it as they do in favor of violence and the threat of violence -- hard power.  Unlike soldiers, ships, and spies (and now drones), everything about soft power is completely compatible with liberal democracy as well, because it is nothing more than engaging in consensual human relationships and discourse.  

There is therefore nothing inherently wrong in any way with soft power or organizations that foment it like the NED, even if it leads in some extreme cases to the eventual toppling of governments like in Egypt (twice), Tunisia, Libya, Yemen, and now the Ukraine. It could only work to such an extreme if there is a genuinely large enough consensus for such an outcome in the first place, quite unlike the kinds of murder, threats, and trickery we associate with the CIA's coups and attempted coups, or the brute violence of even a minor military intervention.  Democracy is so embedded within approaches supported by the NED that an attempt at such a radical end as the overthrow of a government can be easily defeated by the same approaches used by defenders of such a government, if they do indeed have that kind of support (as I expect Maduro actually does in the case of Venezuela today). And since a democratically elected government must have been able to organize the kind of soft power needed to win a national election in the first place, whatever the NED might be teaching need only be feared by leaders who have lost so much legitimacy since their election in one way or another.    

Power of the masses is, after all, what community organizing and grassroots political action is all about -- exercising power through discourse and human relationships instead of coercion through force or violence. And there is nothing inherently problematic about the US engaging in such means of discourse either, because its own polity is completely open to anyone -- people, organizations, and governments of any other nationality -- doing the same kinds of things to contest power with US policymakers and elites within the US.

There are scores of demonstrations and actions every day on the National Mall in Washington, DC, from foreign funded outfits.  And foreign individuals, organizations and governments are allowed to lobby and organize politically as well as any citizen with the recent exception of participating in actual elections.
It's not another example of exceptionalism," in other words.  I believe the same is the case throughout Europe and in Japan and most other liberal democracies as well.  And if it isn't, it certainly should be.

For a big example: Why will the WTO never hold another summit level meeting within the US? Because the last time they did civil society groups converged on Seattle in 1999, and there has not been a single advance in any agreement toward further reducing global trade barriers since. (And yes, there were a few broken windows and molotov cocktails thrown by undisciplined troublemakers in Seattle too, but that's hardly what we mean by "violence".)

So, why, of all groups or people in the world, should Americans, or the US government, be excluded from engagement within civil society spaces around the world?  I mean, in addition to full spectrum dominance of the military, intelligence, and finance, does anyone really believe that US is also so dominant in community organizing (!?) that its citizens and government should be excluded from civil society spaces around the world too? That's a question that needs some exploration.

So, yes, I am quite dismissive of critiques of the NED or any other civil society based organization just because a few of its grantees might end up overthrowing a government someday by organizing the kind of protests which are perfectly acceptable and commonplace, even if also highly controversial and contested when successful, in liberal democracies. Civil society should not be excluded from the set of spaces that may be contested by foreigners in any country.