It is *not* the GPL. It is the Python license http://sourceforge.net/projects/pymol/ see also: http://www.python.org/doc/Copyright.html
I hit the send too quickly, anyways there is a fundamental difference in that derivative works of pymol AFAIK can be made proprietary, not that this would be an advantadge since the current pymol development is so dynamic. Cheers, Zac