elections in April 2014 and the withdrawal of ISAF combat troops post-2014. For a long time many of the NGOs have advocated a separation between the activities of the military and those governmental and non-governmental organizations engaged in the economic development and assisting governance. The NGOs complain that they are at risk of attack by insurgents if they work with or in conjunction with the NATO forces. In addition, there is usually a philosophical difference in approach to resolving conflicts and engaging in conflict that separates the two camps.
There are a few complicating factors that weigh in on the situation. One is that the Taliban have a poor record of observing the norm of not attacking civilians and unarmed non-combatants (see the news on the most recent bombing of a Kabul restaurant). This has, in many cases, forced NGOs to seek the protection of the military to get around the country to do their work. In addition, many NGOs are financed as "implementation partners" of the military and other government entities - so there are ties there as well. The military has also provided a unifying function in the establishment of Civil Military Operations Coordination Centers (CMOCCs) and Provincial Reconstruction Teams (PRTs) at the provincial level. Thus the military has gotten deeply involved in development and governance efforts. Many would argue that the military should conduct these development and governance activities as they are two key lines of effort of counterinsurgency.
Read more on this topic in "German NGOs assess role in post-NATO Afghanistan", EurActiv, January 20, 2014.