As an idiom it dates back at least the beginning of the 20th century. As a concept it goes back a few decades earlier.

The concept is not that the "Captain must go down with his ship". It is that the Captain should be the last to be rescued. This often times results in the captain going down with the ship but that is a result of saving the lives of everyone else first.

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Follow-up question: was there an increase in occurrences of a captain going down with the ship after the execution of Admiral John Byng?

This concept is something of a myth. Although some Captains and Masters have gone down with their ships, in some cases clearly deliberately, there has never been any sort of requirement or expectation that this should happen. In many cases Masters have remained onboard until as many passengers as possible have got away, for example. There have, of course, been many cases where Masters or Captains have been lost in the loss of a ship, but haven't elected to "go down with their ship" but have simply been lost in the course of the foundering or other loss of the vessel. Captain Leach of HMS Prince of Wales (along with the Force Z commander, Admiral Tom Phillips) was lost with the ship, but had attempted to abandon along with everybody else. The Captains of HMS Hood, Jervis Bay, Rawalpindi, Glowworm, Courageous and Glorious, as Royal Navy examples were all lost with their ships, but there is no suggestion that any of them chose to be. Admiral Tryon may have chosen to go down with his ship after the fatal ramming by HMS Camperdown, but there is no evidence for this, and HMS Victoria's captain, Captain Bourke was saved. The only cases I can think of where a Captain or Master deliberately chose not to survive their ship's loss, as opposed to remaining onboard through particular circumstances like Captain Herndon, are the loss of the Titanic, the Laconia and the French cruiser, the Leon Gambetta. In the case of the Titanic it has been assumed that Captain Smith chose not to seek to escape the sinking vessel, but there is contradictory evidence about this, with some survivors asserting that he remained in the Wheelhouse whilst others assert that he was in the water after the sinking. Rudolph Sharp, the Master of the Laconia probably did deliberately go below as she sank. He had been Master of the Lancastria when she was bombed and sunk in 1940, the worst British maritime casualty with the highest loss of life. Admiral Senes and all of the officers stayed onboard the Leon Gambetta when she was torpedoed and sunk in 1915, none of them making any attempt to escape, so it can safely assumed that in this case they certainly did choose to go down with their ship.