No doubt that airplanes consume lots of fossil fuel and generally mess up the atmosphere in a major way. Nevertheless, travelling is hard to avoid if you wanna get anywhere.
My good friend Adam has heard my scruples about flying for years. He pointed me to this article from OnEarth Magazine which tells about a number of organisations that will plant trees for you to offset the effects of your flying.
For instance, a round trip from San Francisco to Shanghai will produce 2.2 tons of carbondioxid emissions. This can (in some more or less abstract sense) be offset by planting three trees or changing three ordinary light bulbs to energy saving ones. Depending on what organisation you choose, for around $20-40 you can have them plant the trees or install lightbulbs.
Among the organisations are American Forests, which have an online Climate calculator that will give you a sobering view at the side effects of transportation.