I am afraid the article is right about Star Treks concern with terrorism since the late 1980ies. There where countless TNG-Episodes dealing with terrorism, even in the early seasons of TNG.
In the first season there where many episodes dealing with rebellion, like 'Angel One' and 'Heart of Glory', or weapons trade, like in 'Arsenal of Freedom'.
In the second season there was 'Samaritan Snare', which dealt with development aid for an underdeveloped culture, who tried to aquire weapons by taking hostages (stupid Paklets, stupid
Thats when 'Star Trek : The Final Frontier' hit the theaters, giving us a gang of religious fanatics who take hostages and hijack the Starship Enterprise to meet their creator.
In season three of TNG it was 'The Vengeance Factor', dealing with tribal warfare and blood feud in an assymetric war between a technically advanced and a pirate like rogue faction.
Then there was 'The Hunted', sporting a Space-Vietnam-Veteran turning into a "Terrorist".
The first real Terrorism-Episode was 'High Ground' in the same season, again about assymetric civil war between an advanced ruling faction and a rogue organization, operating from the underground. The episodes trailer even opened with a terrorist bomb attack against a public square not unlike a nowadays shopping mall.
In the fourth season there was 'Legacy', about a civil war fought with guerilla tactics, but most important, there was 'The Wounded' which got the whole Cardassian-Bajor-Marquis-Ark getting started.
In season five (shortly after Roddenberrys death) this ark got about terrorism very explicitly with the episode 'Ensign Ro'. That episode had the Enterprise hunt down terrorists and even implemented metaphorical similarities to the Israel-Palestine-Complex (namely depicting Bajorans as refugees, living in desert camps and one of their "Terrorist" Leaders wearing a tunic and a headscarf).
I think people allways forget that the tragic surprise of 9/11 was in its shocking magnitude, but not in the fact of a terrorist attack itself, because terrorism was indeed a very present phenomenon and topic throughout the 80ies and 90ies. It was politics to make us all forget that long history that came before and lead to 9/11.
Roddenberrys TNG does indeed show parts of the impact terrorism and the mid-east-conflicts had on western popular culture throughout the 80ies and 90ies.