Some points to consider:

The Al Queda terrorists and even the Taliban fighters were NOT soldiers of a sovereign nation state. Al Queda is of course an international terrorist organzation and the Taliban was the theocratical terrorist mafia gang that controlled most of the territory of Afghanistan but was never recognized internationally as a legitimate government. Thus these captured fighters - all of them - are simply terrorists and not soldiers of a country. They are not covered under the Geneva Conventions, for the same reason that, for example, Colombian narco-terrorists fighting the Colombian government wouldn't be covered under the Geneva Conventions, even if they controlled wide areas of the Colombian national territory, and were captured by American forces working together with the legitimate Colombian government.