This is a great question to consider because it forces you to look at a situation from different perspectives. In fact, there is no straightforward answer to this. To one person, someone could be considered a freedom fighter. To someone else, they are a terrorist. Because of this, there has seldom been a solid agreement on just what defines a terrorist or freedom fighter.
Some may try to define militia members as terrorists based on international laws and conventions of war. But this is where it grows fuzzy. Terrorists and freedom fighters typically employ similar guerilla-style tactics. At face value, they are hard to differentiate. If you are really looking to see the difference, you need to consider their targets. According to most definitions, terrorists attack nongovernmental targets, including civilians and their property. They attempt to strike terror into their enemies by ignoring conventions of war. Strictly speaking, guerillas are differentiated from terrorists because they restrict their targets to military or governmental ones. A militia that limits its targets to non-civilian ones could still earn the title of terrorist, though. A government or military that has been attacked by so-called freedom fighters would most likely label them as terrorists.
Technicalities aside, the real difference depends on one's point of view. Nelson Mandela was labeled a terrorist by the apartheid government of South Africa. Yet, he was fighting for the freedom of his people. For his part, Mandela claimed the apartheid government was the terrorist. As you can see, it often comes down to which side your loyalties and sentiments lie on, since they are effective labels of propaganda.