Whether it's being used to power the Enterprise or destroy the Vatican, antimatter remains perhaps the most potent energy-producing substance for which we have a theoretical basis of understanding. In some respects, it seems almost tailor-made for the energy needs of a spacefaring society - almost the petroleum of the spaceways, if petroleum needed constant monitoring and intervention to keep it from catching on fire. You'd have to be absolutely insane to use it anywhere other than space.
So far, we've only been able to study antimatter in fits and starts - but this won't always be the case. Yesterday, CERN announced the successful trapping of antimatter atoms through the use of magnetic fields, presumably the first versions of the containment fields that always have to collapse before the warp core will breach. Sure, they hung around for less than a twentieth of a second, but it's a start. This is another step toward the frontiers of science, and I'm looking forward to many more.
One thing I haven't yet seen are far-out conspiracy theorists or 2012ers integrating this into their fantasies - but it's only a matter of time. I've already encountered people concerned at whether taming antimatter would add palm-sized city-busters to a terrorist's arsenal.
Technically - yes. But the reality is more complicated.
Antimatter needs to be contained within magnetic fields because if it ever encounters regular matter, the two will mutually annihilate in a burst of gamma rays and other fun things. This also liberates a massive amount of energy. How massive? One kilogram of antimatter annihilating one kilogram of matter would create a forty-three megaton explosion, not much weaker than the single largest nuclear weapon ever detonated - and the advantage of implosion-trigger nuclear weapons is that they will not accidentally detonate. Any antimatter warhead, or antimatter reactor for that matter, would require constant attention to ensure that the containment fields would not collapse. So, even if someone was able to cobble together a two-kilo city-buster, if they didn't build it right it might well go off in their face.
Realistically, though, there's one thing that stands in the way of anarchists hurling around antimatter bombs: the expense. Just as it's the most potent substance known to humanity, it is also the most expensive - in the ten years between 1991 and 2001, the antimatter synthezised by CERN, one whole nanogram, cost "hundreds of millions" of Swiss francs - and you'd just need 999,999,999,999 more in order to build your city-buster. Remember that CERN is studying individual atoms of the stuff. It may well be far, far more economical to send spaceships to harvest the antimatter that occurs naturally in the Van Allen belt.
What this all does mean, though, is that as antimatter becomes marginally easier to collect and retain, it will have to become the single most controlled and restricted substance in civilization. Cost is the biggest barrier, but you can't count on a big cover charge keeping everyone out. For the foreseeable future, worrying about antimatter attacks is pointless; anyone who would be able to assemble enough antimatter to be a threat would also be able to buy a nuclear arsenal, pretty much.
Until then, may your warp cores never breach.