First up it is great that you are aware of the impact flight has on the environment. Aeroplanes travel in the sensitive upper atmosphere and release a cocktail of greenhouse gas emissions which are a major contributor to global warming. There are ways that you can repair your trips contribution to global warming. Check out http://www.climatecare.org/responsibletravel/. You can offset the cost of your carbon emissions to help fund projects on renewable energy. (Reducing emissions by the same amount as your share of the flight creates.)

Purchasing carbon offsets is a great way to reduce your carbon footprint in general, especially for air travel.  I like the website http://terrapass.com because it allows you to calculate your total carbon footprint and allows you to purchase offsets.  They show you up front what the money you spend will be used for and also provide items for purchase which you can use around your home to help reduce your total carbon footprint. 

Another way to reduce your carbon emissions for travel would be to look into how airlines themselves work to reduce their emissions.  You can then make the decision to use the airline with the best practices and least carbon output.