NGO's that operate on their own budget rather than at the expense of the taxpayers are fine, and I wholeheartedly support the missions that many of them undertake (Doctors Without Borders, as mentioned above, immediately springs to mind). These groups serve a valuable purpose and because they operate on their own budget are free from unnecessary political influence from the state while fulfilling their mission. Some groups may also have a hidden agenda, that when operating may in fact be a detriment to the local populace (religious evangelicals who proselytize as their primary activity come to mind) and if are funded by the government they may easily be perceived as operating at the behest of the government and may even overtly represent themselves that way making deniability of their 'orders' difficult, at the very least.
It is of tantamount importance that Americans, as citizens and residents of the world, come into contact with other cultures as a benefit to both the US and the other culture. Far too few Americans speak any language other than English and the cultural isolation this brings about, not to mention the limit to thinking (as it is extremely hard to create a concept in one's mind that cannot be verbalized by most people) is a strong handicap we as a country have as we move deeper into the 21st century and do so without as many direct connections to other cultural groups as other cultural groups have among themselves.