No, I actually agree that many of these militant groups should be classified as military organizations, and thus subject to the Geneva Conventions on POWs when they fall under US custody, as a high contracting power.
"The Convention shall also apply to all cases of partial or total occupation of the territory of a High Contracting Party, even if the said occupation meets with no armed resistance."
Afghanistan, Iraq, and Libya have all been High Contracting Parties since 1956. The Geneva Conventions of 1949 are the Supreme Law of the United States under Article VI, Paragraph 2 of the Constitution of the United States, and have been since their ratification on February 8, 1955.
So, it's good to see y'all agreeing with me that every prisoner the US has taken during the War on Terror should be accorded the protections of the Geneva Conventions. I urge you to petition your congressional representative to allow the prisoners to receive and send mail, that torture against them be strictly prohibited, and that we live up to the standards to which we as a nation agreed, and that they be allowed free access to the court system when those rights are denied, given your evident concord with me regarding their rights.