They are called "terrorists" because they engage in what is commongly understood to be acts of terrorism. While there are many competing definitions, the most commongly agreed on involves:
- Use of violence
- To achieve political goals
- Perpetrated deliberatly on non-combatants (note the intent and the target).
E.g., Wiki states:
Since 1994, the United Nations General Assembly has repeatedly condemned terrorist acts using the following political description of terrorism:
"Criminal acts intended or calculated to provoke a state of terror in the general public, a group of persons or particular persons for political purposes are in any circumstance unjustifiable, whatever the considerations of a political, philosophical, ideological, racial, ethnic, religious or any other nature that may be invoked to justify them."
A definition proposed by Carsten Bockstette at the George C. Marshall Center for European Security Studies, underlines the psychological and tactical aspects of terrorism:
Terrorism is defined as political violence in an asymmetrical conflict that is designed to induce terror and psychic fear (sometimes indiscriminate) through the violent victimization and destruction of noncombatant targets (sometimes iconic symbols). Such acts are meant to send a message from an illicit clandestine organization. The purpose of terrorism is to exploit the media in order to achieve maximum attainable publicity as an amplifying force multiplier in order to influence the targeted audience(s) in order to reach short- and midterm political goals and/or desired long-term end states."
Therefore, the partisan groups in Afghanistan who target and kill civilians (and only those groups) are commongly called terrorists.
Before you start screaming and ranting about "American biases", they are actually VERY consistent in the application of that definition:
Northern Alliance groups, who to the best of my knowledge restricted their intentional warfare to combatants (first, Soviets, later, Taliban), were never referred to as "terrorist".
Taliban, who engaged in systematic acts of intentional violence against civilians, are terrorists, no matter what their military/political objectives are. Brief Wiki perusal quickly leads to easy examples:
According to a 55-page report by the United Nations, the Taliban, while trying to consolidate control over northern and western Afghanistan, committed systematic massacres against civilians. UN officials stated that there had been "15 massacres" between 1996 and 2001. They also said, that "[t]hese have been highly systematic and they all lead back to the [Taliban] Ministry of Defense or to Mullah Omar himself". Al Qaeda's so-called 055 Brigade was also responsible for mass-killings of Afghan civilians. The report by the United Nations quotes eyewitnesses in many villages describing Arab fighters "carrying long knives used for slitting throats and skinning people".
 Newsday (October 2001). "Taliban massacres outlined for UN". Chicago Tribune.
 Newsday (2001). "Confidential UN report details mass killings of civilian villagers". newsday.org. Retrieved October 12, 2001.