Ohh! Something I may have an answer to.

I think the question may stem from a misunderstanding concerning generals and admirals. While in the modern day, and even by the 18th century, a general commanding a fleet or even a ship would be seen as ludicrous, this was far from the truth in the 16th and early 17th centuries.

At the time of the Spanish Armada, centralised state fleets were a rare occurrence in Western Europe. The English fleet that fought the Armada is a case in point - a hodge podge collection of merchant ships, privately owned privateer vessels, as well as Royally owned ships. Their organisation was haphazard at best and naval warfare quickly descended into brawls aboard ships in a wild melee.

And who's great for fighting in a melee? Even one aboard ships? Soldiers! For centuries it was considered vogue to pack your ships with as many soldiers as possible in the lead up to a battle, and the primary tactic was the engage, board and overwhelm your opponents. The line-ahead broadside tactics of Jervis were far in the future at the time the Armada. It should be noted that the Spanish were fond of packing their ships with soldiers even after broadsides became more powerful - many of their disproportionate casualties at Trafalgar may be partially explained by this.

I digress. Essentially Generals were considered apt for command of large fleets at the time of The Armada because large fleets often had huge numbers of outright soldiers. It should also be noted that the Armada was an invasion fleet - a General would be considered best to command an invasion once it hit the ground anyway.

Admirals didn't come into their own until long after the battles at Gravelines. In fact, the Napoleonic era rank of 'Master' is a call back to this period. For centuries the captains of ships were often simply gentry or military men given command of a ship in wartime. The man responsible for actually sailing and directing the ship was it's Master. In the Napoleonic period these masters were still around, albeit at a time of transition when Captains were becoming more than competent sailors in their own right.

Will post more sources when I'm off my phone!

Lewis, Michael. The Spanish Armada

Rodger, N. A. M. The Safeguard of the Sea: A Naval History of Britain 660–1649

Pierson, Peter. Commander of the Armada: The Seventh Duke of Medina Sidonia.

Parker, Geoffrey. "Why the Armada Failed." History Today 1988