Remember, ships are powered by a limited amount of a power, so using conventional projectile weapons does sort of make sense. You can't just go around firing massive bursts of matter and anitmatter at everything that attacks... it takes energy to deal out energy... So it makes sense to fling something out of your ship that doesn't reduce your available power, but still delivers a massive punch. You don't want to make things so alien that people won't immediately know what they are... if power were unlimited, why not just lock on to the entire outer hull of your adversarial ship and beam it away, exposing the entire crew to the vacuum of space? Why? Because that's not realistic (and it would make for REALLY boring space battles).