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Good question,, just been on a 2000 mile round trip to the glaciers in france in an '-5 Ford Focus.
Think looking at bills its cost about 5mpg on motorway driving. The benefits over a roofrack are amazing though. Thule are rated at about 75kg load so we had 5 pairs of skis, all our boots and then back protectors in which really free'd up space in the car and made it a relatively comfortable drive.
The other great thing with the Thule system is that it takes literally 2 minutes to get the box off and maybe 5-10 mins to take the bars off each time so it really isnt that much of a hastle if you want to save on gas when you're not using it. Buy one, you wont regret it!