The patent in question is http://www.freepatentsonline.com/7640098.html (source: http://news.priorsmart.com/stenbock-everson-v-runwayfinder-l... )
To summarize: it's a patent on the idea of overlaying a flight plan on a map using a website. The general case of this is drawing line-segments on a background, something every trivial paint program can do. This patent clearly fails the obviousness test.
However, what is USUALLY the case with patents is that they are far narrower than what is claimed by the company or in the press. "Company patents pencils!" says the news article. When you read the patent you find that they've patented a very, very, very narrow use of pencils and that few, if any of the world's pencil uses are encompassed by the patent.