AMir
I know nothing about laws and even less
about Patent Laws .. Still reading what FLAC is I don't seem to see the problem with its commercial use.. Some more knowledgeable should try to explain but I lean toward a more plebeian explanation: A refusal to give more wind to the free software movement...
Let me give you an example. We designed VC-1 as a next generation video compression format. Like FLAC, we wrote the specification, implemented it in code and license it to others. As a requirement for submission and eventual mandatory status in Blu-ray, we were asked to provide the specifications to a standards org which we did (SMPTE). That led then to a third-party licensing company who did a call for anyone who may have patents which read on it. A dozen companies showed up and after their patents evaluated, they were all deemed essential and become part of the licensing group. Their claim was that they had basic patents that read on any implementation of a transform based compression engine. Indeed, the same patents are part of the pool for MPEG-2, MPEG-4 and VC-1.
Same is potentially true of FLAC. It uses linear prediction to compression data. Such a technique has been used by compression engines before it. I can't tell you if some has or has not patented them. But if I were a betting man, I would say more than one person or company would lay claims against it as soon as a major company with deep pockets implement it.
Open source in general has less of this risk in that if I just write some software it is much less likely that someone has a patent on it. That said, there could be claims there just the same as we have seen from lawsuits from Microsoft and others against open source operating systems.