American Indians in the 19th century and before most certainly fought back against white settlement frequently, tenaciously, sometimes effectively and very often unmercifully; the "Indian massacre" and scalping, staples of the movie and television Western, were real things. It's just that the pop culture left out the inconvenient details that those massacres were often
responses to white settler massacres of the Natives and that scalping in fact was a European innovation that the natives adopted in retaliation.
That's a story repeated in anti-colonial struggles across the planet; Indian Mutiny, Boxer Rebellion, Mau Mau Revolt, various Irish rebellions and conflicts, you name it. And if the term "terrorist" had existed to be lobbed at those resistance groups in those times you can be 100% sure that it would have been, just as it was at the ANC and Umkhonto we Sizwe in South Africa. And of course many of those groups really were bloody and unmerciful and less than scrupulous about the fates of innocents (umKhonto we Sizwe not excepted, though they were more careful and restrained than the likes of, say, the Mau Maus)... sometimes because their enemy was also unmerciful and they were fighting for survival, sometimes because they were opportunists for whom the fight against colonialism was an excuse to augment their own power, more often a mixture of both.
Of course groups that were so massively outgunned and repressed that they could face wholesale lynching or expulsion for simply spitting on the sidewalk at the wrong time were less prone to violent resistance; although it's actually a fallacy that Blacks never fought back during slavery, there was never large-scale uprising for that reason, in large part because the example of Haiti had so terrorized slave-holders in the Western hemisphere that they cracked down extra-hard to prevent its repetition. But that's not necessarily because they were more innately virtuous or less proud than any other groups, it's because their circumstances were different. And often when their circumstances were changed -- the Americo-Liberians in West Africa, the Zionists in the Middle East, both of whom were populations essentially compelled to hew out their own states on account of being largely unwanted elsewhere -- they in fact did
not hesitate to employ forms of violence that could be labelled "terrorism."
There are noteworthy exceptions, but they're context-dependent and often different from popular imagining. Take the holy trinity of modern Princes of Peace who are now routinely brought up in this context:
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Gandhi and satyagraha in India, for example, happened for two major reasons (over and above Gandhi's personal faith and morality): one, that Gandhi clearly perceived that violent overthrow of the colonial order could easily lead to catastrophic communal violence afterwards (which happened anyway, but at least he tried his level best to prevent it); two, he understood that due to the tiny British presence in the country, a nonviolent movement with sufficient cohesion was capable of simply shutting the whole country down, which really was the most devastating weapon in his arsenal.
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Martin Luther King used similar methods to exploit a different weapon, the power of mass media to expose and embarrass injustice and move constituencies both internationally and domestically into support of the Civil Rights Movement.
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Nelson Mandela, now remembered for reconciliation and understanding -- which were indeed very crucial parts of his legacy -- also embraced "armed struggle," labelled "terrorism" by his enemies,
and never renounced it. For very good reasons, including that during the negotiations leading to the end of Apartheid, the Nationalist government tried to use Buthelezi's Inkatha Freedom Party as a "third force" to weaken the ANC's bargaining position by killing its supporters en masse. Tens of thousands of people died in the ensuing violence, largely forgotten in the West today and written out of the popular Mandela story (which now is about Morgan Freeman ending apartheid by supporting rugby

).
Of course it's right to oppose communal violence and bombing in an ideal world, but it's not right to elide the reality that many of these struggles don't take place in an ideal world. "Terrorism" is an epithet that tends to be conveniently thrown at "freedom fighters" who are attacking one's own side, whether that side is right or wrong, and to demonize the enemy in order not to have to think about the real sources and consequences of conflict. It's still common to encounter Brits who use language about the Nazis to damn the IRA / PIRA during the Troubles while conveniently forgetting that that particular round of violence was started and usually escalated by Loyalist militia groups and by the British military. That kind of blind spot persists to this day; which is not an excuse for groups like ISIS or Boko Haram, which are genuinely awful, it's just a reminder that evaluating their existence and actions without context is stupid and useless.
Trek, and especially DS9, was absolutely right to take a broader and more nuanced view than that.