I think it's dependent on the situation. We've been very much caught up in Afghanistan and the particular examples of Afghanistan.
Situations are different in different parts of the world and that fact must be recognized. In some cases, it is perfectly safe for NGOs to be working in many parts of a country. In others, it is very dangerous and it is wise to work in closer cooperation with the military, the United Nations, or with whomever can provide a measure of security. Each situation has to be assessed on its merits.
In the case of Afghanistan, we can see that some NGOs are very comfortable working with the military. These are not necessarily humanitarian organizations. Members of humanitarian organizations who see the military when they are working to distribute assistance or working with the people may consider that the presence of the military puts a target on their own backs. Military and humanitarian personnel have to be aware of that. Other organizations are working in governance or to support the government administratively. They are able to work with the military very easily.