The notion of Humanist/Atheist chaplains makes me rather uneasy. I do understand why those pushing for it find it necessary to do so. I do not want to belittle those intentions and efforts but there are some serious issues that should not be set aside.
I would start by pointing out that a common definition for chaplain (in terms of military) is, "a priest, minister, or rabbi attached to the armed forces." This has been expanded over the years to include a wider variety of religions but all chaplains represent a religion. This is where my first concern comes in. Atheism is not a true "ism" let alone a religion. I can easily see the push for chaplains being used to confirm and further push the myth that atheism is really just another faith. By definition it not only is not a religion it can not become one. It is the absence of a supernatural belief system featuring a god or gods. Some may argue it is a game of semantics but they would be wrong. Words have meaning for a reason. We could not communicate and express anything without them. Outright changing the definition of something to suite your own specific goals is not a matter of semantics.
The other major problem I have is that this push could also be used to further blur the concept of separation of church and state. I have never been comfortable with taxpayers footing the bill for military chaplains. I understand that our soldiers have a right to worship and stay connected to their faith no matter where they are performing their military duties. But, why should we pay for it? The various churches, mosques, etc. should be paying. After all, it is their faith community being served by the chaplains.
With those two objections in mind I would point out that I do agree with many points made by the advocates of Humanist/Atheist chaplains. Our servicemen and women are themselves grossly under-served. In many instances the only thing resembling psychological or social services are being performed by chaplains. If a soldier or officer is in need of counseling of any type they should have access. It should not be by chaplains unless the individual sees the problem/issue as one of faith. I also acknowledge that the chaplaincy can convey a number of privileges that would otherwise be lacking. Non-religious personnel should not be deprived simply because they are non-religious. There are issues of equality that need to be addressed. I just don't think it should be through chaplains.
I realize that many of the services and privileges non-religious military personnel currently are lacking are not likely to be gained through any source other than the chaplaincy until military policy and practice are changed.
Perhaps the push for including non-believers will lead to greater reforms in military personnel services. I hope it will. If that does not occur I fear that if non-religious gain their own chaplains it will end up hurting the non-religious community in the long run.