I'm in love with Jesus and proud of it!
Fuel rod guns fire a bolt of irradiated material, similar to a plutonium rod used in nuclear power plants (irradiated plutonium actually glows greenish yellow). The material is highly reactive and unstable, and explodes violently on impact. It's called a "fuel rod" because that's what it is, a fuel cell for a nuclear reactor.
Hunters appear to use a heavily modified variant of the FRG, with the weapon (and ammo supply) integrated directly into the Hunter's armored suit.
In older Halos it was a bolt of energy, not a stream like in H3 and Reach. However, in ODST there were two types of Hunters, blue and gold. Blue Hunters shot the beam and gold ones shot a bolt.