Charged particles can't be used in air. In outer space, they can be deflected by electric or magnetic fields. A collimated beam will also become defocused by ambient fields over a sufficiently long distance -- and the distances are typically very long in outer space. If you make a beam of, say, negatively charged particles, then conservation of charge says there are also some positively charged particles -- what do you do with them? Charged particles are not very penetrating, so it's easy to shield against them. For example, MeV electrons stop in a piece of cardboard.
A general problem with any particle beam weapon is waste heat. For instance, at a heavy-ion accelerator where I used to work, the beam would typically be about a watt, whereas the accelerator probably used many kilowatts. I.e., accelerators tend to be the most fantastically inefficient devices ever created. In the classic battling-spaceships scenario, the efficiency of the ray-gun would have to be incredibly high, or the gun would just destroy its own ship with waste heat. (This issue also applies to relativistic propulsion of a ship.)
Antimatter would annihilate with matter in the target, producing a devastating explosion if there was any significant amount of it. Charged beams of antimatter are relatively easy to produce, but suffer from the same problems as other charged-particle beams. Neutral antimatter is extremely hard to produce; nobody has ever made more than a tiny number of antihydrogen atoms. If you could produce it, you wouldn't be able to accelerate it with electromagnetic fields.
In real life, satellites and other space vehicles are extremely flimsy and vulnerable things, and the kinetic energies involved are very high. It's very difficult, for example, to keep the ISS from being destroyed by stray space junk. This is one of the reasons that the type of space-based weapons envisioned in SDI (Reagan's "Star Wars" program) are fundamentally a pretty stupid idea. It's really easy to knock them out by hitting them with a small bullet moving at high speed. Countermeasures also tend to be much cheaper than the weapons themselves.
[EDIT] Fixed my totally incorrect analysis of antimatter.