Nitrogen is inert and doesn't affect rubber or the steel rim. Carbon dioxide is highly reactive and affects both the rubber by causing swelling in the rubber. It also would cause corrosion in iron based rims (particularly Carbon- Steel).
Edit: When CO2 is mixed with moisture becomes Carbolic acid which is corrosive. It all depends on concentration. It is like comparing Acetic Acid commonly referred to as Vinegar. At 3% you can put on french fries. At industrial strength 97% not only will it dissolve the french fry but also human flesh right down to the bone very fast. As for CO2 affect on rubber I cited a industry source-(Air Liquide) a company that specialized in compressed gases.
In the case of automotive tires using CO2 would probably cause catastrophic failure. My experience with Nitrogen is that I have noticed it to be much more quieter while driving and less pressure variations when the temperature varies from season to season.
http://encyclopedia.airliquide.com/encyclopedia.asp?LanguageID=11&GasID=26
Check under Material Compatibility under the heading of Elastomers- Quite illuminating.....