What other freedom is there? The freedom of the majority to tamper with the freedoms of the minority?
A "free society" as we think of it is definitely based on freedom of the individual, yes.
Neither group nor individual freedoms ought to take a blanket precedence. The question is one of utilitarianism; what creates the greatest good for the greatest number? If that is an individual right that diminishes a group right, then the individual right's value must outweigh the group right's value. In free speech, it usually does. In overfishing, it doesn't.
One could argue that this in itself is a breach of other's individual rights; I believe that no individual rights should be impeded on, as long as they are not impacting the individual rights of others in a meaningful way. If that's what you mean.