Commanding Petty Despots: The American Navy in the New Republic tells the story of the creation of the American Navy. Rather than focus on the well-known frigate duels and fleet engagements, Thomas Sheppard emphasizes the overlooked story of the institutional formation of the Navy. Sheppard looks at civilian control of the military, and how this concept evolved in the early American republic. For naval officers obsessed with honor and reputation, being willing to put themselves in harm's way was never a problem, but they were far less enthusiastic about taking orders from a civilian Secretary of the Navy. Accustomed to giving orders and receiving absolute obedience at sea, captains were quick to engage in blatantly insubordinate behavior towards their superiors in Washington. The civilian government did not always discourage such thinking. The new American nation needed leaders who were zealous for their honor and quick to engage in heroic acts on behalf of their nation. The most troublesome officers could also be the most effective during the Revolution and the Quasi and Barbary Wars. First Secretary of the Navy Benjamin Stoddert tolerated insubordination from "spirited" officers who secured respect for the American republic from European powers. However, by the end of the War of 1812, the culture of the Navy's officer corps had grown considerably when it came to civil-military strains. A new generation of naval officers, far more attuned to duty and subordination, had risen to prominence, and Stoddert's successors increasingly demanded recognition of civilian supremacy from the officer corps. Although the creation of the Board of Navy Commissioners in 1815 gave the officer corps a greater role in managing the Navy, by that time the authority of the Secretary of the Navy--as an extension of the president--was firmly entrenched.
This book isn't a full history of the early American navy; it's a history of civil/military relations in the Navy, from the Revolution through directly after the War of 1812 when the situation was regularized into something approaching the current setup.
At the beginning, with only a few individual ships and confused lines of command (through General Washington, different Congressional committees, and state authorities), individual captains were selected for fighting spirit and a strong sense of honor, and granted great latitude. This culture continued through the Quasi-War, with captains flouting orders for the sake of their honor and everyone shrugging. Sheppard points out this system had vanished by the Embargo and War of 1812, and argues it ended with Jefferson's reduction in naval strength. However, while that was probably important in changing culture, I'd say another element he mentions was at least as important: the growing number of naval commands (especially with Jefferson's gunboat armadas), leading to more important naval institutions.