Different kinds of free though.

Calibre developers chose (either consciously or through ignorance) the GPL licence, which means free as in free speech. Nobody should be able to distribute programs based on the Calibre code without also releasing the source. Hamstersoft software, however, is free as in free beer (since they don't distribute sources, claim there are trade secrets in their software etc.).

According to that article, that particular case had nothing to do with Google's patents. It was in fact company called Traffic Information that sued several companies producing web street maps. Google became involved when Traffic Information notified T-Mobile that Google Maps traffic feature was infringing their patents.