One time I worked on a power grid simulation that wanted to release its code but it couldn't because it used algorithms from «Numerical Recipes: The Art of Scientific Computing» which has a pretty asinine copyright policy with respect to openness : http://www.nr.com/com/info-permissions.html

Even worse are the researchers who keep their models and data sets secret due to paranoia that some colleague will publish first, which admittedly does happen.

Cultivating a spirit of genuine cooperation and sharing in academia would do wonders for the progress of the sciences, but there are so many hurdles that need to be removed. It's not just a matter of knowing that it's good to release source code or feeling confident in including it as the article suggests.