I think that the two main (functionality-based) reasons that people will use one over the other in different situations are:
* CO2 doesn't lose as much pressure when it's cold out. So if you're playing outdoors in the winter, you'll have less pressure (sometimes not enough pressure to even cycle the gun) with green gas. CO2 doesn't have this problem. Similarly, if you fire a gas gun fast enough, the green gas "cools down" and again, will cause problems with not having enough pressure (the cool down effect).
* CO2 magazines only require that you replace the CO2 canister. This means that when you head out on the field, you can just toss a bunch of CO2 canisters in a pouch, or put them in a shotgun card, etc, and "re-gas" your mags on the field. Green gas would require you to carry around a propane tank, or something that's usually more bulky than little CO2 canisters.
Green gas is usually the cheaper, easier way to go. Green gas is just propane, really, so you can buy those little coleman propane tanks for $3, and get a LOT of mags out of it.
I also prefer to stick the green gas nozzle into my mag and press, rather than open the mag and screw in a new CO2 canister, but that's just laziness. =P