It is inevitable that in a book about the British Navy in the 1800's that the subject of class would be a recurring idea.
The most dominant theme of class in Master and Commander is probably on the Sophie, where the officers reign over the crew with audacious and unrelenting power. This power is fully supported and enhanced by the Articles of War, which treat most types of insubordination as a capital offense. For lesser offenses, a public flogging is the preferred methodology.