There are loads of thread on this purpose, a little searching does nowone any harm.
But I'll tell you anyway.
The big difference between air and Co2 is that air is compressed air, that is regulated from 3000 or 4500psi to 800psi but Co2 is liquid Co2 that is held at pressure, and expands to create the gas your marker runs on.
Most people consider air to be better because it is very concistant and isnt affected by temperature, like co2 is. Also its a lot cleaner, a lot of dirt and grime can get into Co2 and so gets into your marker and clogs it up.
Though a lot of people use Co2 on markers like the matrix and shocker because it gives a lot more shots per fill than air.
Co2 will give a lot more shots when compared to an air system of equal size, because of the fact it's a liquid. But there are some very large air systems that can give just as many shots, but they are quite combersome.
In the long run people prefer to use air because of its concistancy (sp?) which can be read as increased accuracy.