The book
Flying Fortress: The Story of the Boeing Bomber, published in 1943 and written with the assistance of, among others, Boeing's chief engineer at the time, Edward C. Wells, provides this claimed origin for the B-17s' name:
Thomas Collison wrote:
It was while the Grandfather was being built that the little group of "believing men with an idea," the people who had fought through the lean and hungry years when the fate of the entire Boeing organization was in doubt, gave Grandfather and his illustrious family a name.
"It's as big as a fortress," someone remarked.
"Sure it is," another man replied. "It can fight like a fortress. You might say it's a flying fortress."
You might say it! The world has been calling it a flying fortress since that day.
(Source: Collison, Thomas.
Flying Fortress: The Story of the Boeing Bomber. New York: Charles Scribner’s Sons, 1943, 16-17.)
While the anecdote reads a bit too much like marketing spiel to be a perfectly authentic recounting of events, it is interesting in the context of another section earlier in the same chapter:
Thomas Collison wrote:
The original idea for the Flying Fortress was born aboard a battleship.
Back in 1930 Clairmont Egtvedt, then vice president of the Boeing Company and now Chairman, frequently flew from Seattle, Washington, to San Diego, California, where Boeing fighters were based, to spend the weekend chatting with his friend, Admiral Joseph Mason Reeves, commander of Aircraft Squadrons of the Pacific Fleet. They spent many pleasant evening hours aboard the old aircraft carrier, the U. S. S. Langley, as it was tied up at North Island, discussing the nature and use of America's weapons of defense.
Admiral Reeves pointed out that the Air Corps had nothing to offer in the way of a heavy load-carrying weapon that could be compared to the battleship.
"The battleship," Admiral Reeves said, "is the backbone of the Navy. It is the only vessel capable of delivering a final knockout blow to the enemy that dares to attack our country."
At the time naval airplanes were toys compared to the fighting power of battleships of the sea. The Navy's heaviest planes were slow and clumsy patrol bombers which carried only small loads of bombs. The heaviest carrier-based planes were the 90-mile-an-hour torpedo bombers. Dive bombing was just coming into its own. The total weight of bombs that could be laid down on an enemy by America's Naval airplanes was very small indeed compared to the tons of destruction each rifle of a battleship could discharge. And the dive bomber had only a short range.
Was not military aviation being regarded in too limited a sense, Claire Egtvedt asked himself. In the Navy, centuries of experience had developed the battleship as the long, powerful right arm that defeated the enemy. Would there not be greater security for America if she had in the air, as on the sea, a super-weapon which could reach far out and beyond the close-range combat arenas to defeat the enemy before he reached our shores?
(Source: Collison, Thomas.
Flying Fortress: The Story of the Boeing Bomber. New York: Charles Scribner’s Sons, 1943, 12-13.)
Given the fact that this book lists three employees of Boeing in the acknowledgements, who would presumably have had first-hand experience with origins of the B-17, it seems likely that although a recreated conversation, it is substantively a true story. Further, it is clear from the publication of this book that the company had appreciated the marketing significance of the name and fully embraced it. While it was not technically written by Boeing, it might as well have been given the repeated praise the author lays on the airplane and the substantial contributions to it the company made. (No less than 53 of the 124 photographs came from "Boeing News".)
However, the key point is that, in the context of this book, when the unnamed employee remarked that "it's as big as a fortress" he was recalling the battleship.
As an aside, the "Grandfather" referred to above with a capital letter is the Boeing 299. Interestingly, this name is quite similar to the "Grandpappy" appellation awarded to the XB-15 built by the company. It seems likely there is a connection between the two names.
EDIT: Reading a little bit farther into the book, the following paragraph appears:
Thomas Collison wrote:
During this time Boeing engineers had not been sleeping on their laurels. They had all the while been developing a super-fortress, the XB-15.
(Source: Collison, Thomas.
Flying Fortress: The Story of the Boeing Bomber. New York: Charles Scribner’s Sons, 1943, 24.)
What is interesting about this statement is that although the Model 307 is mentioned in the book, the B-29 is not, as at the time the book was published in 1943, it would have presumably still been relatively secret. (The most recent entry in a week-by-week list of notable missions is a raid on Tunisia on 5 February 1943 - thirteen days before the second B-29 prototype was destroyed in a crash during its first flight. This gives an approximate idea of when
during 1943 the book was written.) It demonstrates that the term "superfortress" was in use years before the B-29 entered service.
EDIT: A quick correction: It seems the most recent mission mentioned in the book was actually an attack on the port of Rotterdam on 4 March 1943. However, the author must have forgot that the year changed after December, as all of the 1943 entries are typo'd as "1942".