These Geneva Conventions only apply to those that can be clearly identified as soldiers. This is defined within these conventions and within the Protocols. The Taliban, not being recognised as the legitimate government of Afghanistan, and Al-Qaeda are regarded as non-state actors AT BEST. The US made a determination that members of these two organisations did not fit the description, provided under the Protocols, for non-state actors and are therefore not subject to the limitations of the Convention or the Protocol.
This was in order to try them in US courts, which is not permitted under international law for PoWs. They do not qualify as civillians because they were taken in arms. Ironically it was countries like Iraq and Afghanistan, Sudan, Yemen, etc. who were the most opposed to widening the definition of a non-state actor in order to, for example, use nerve gas on their populations or ethnic cleansing or to enable them to use torture techniques more in line with a real definition of torture. One favoured technique is to nail a prisoner's hands to a heavy table or wall mount and then sever the fingers a joint at a time with bolt cutters; this is very different to water boarding.
The Geneva conventions only apply to civillians and soldiers of legitimate governments recognised by a majority of the UN- it does not protect freedom fighters, partisans, terrorists or any other term you wish to use. The Protocol extends the Geneva Conventions to civillians supporting these movements- civillians being strictly defined as not being in possession of weapons and not being taken in company of others possessing weapons. A legitimate non-state actor must meet many qualifications, all of which Al-qaeda fail and most of which the Taliban fail. It is an all or nothing definition- which is why no nation has attempted to suggest that they are before an international court.