Whoa, really good question. Tough one.

First, the paragraph in question, for those searching:

One of the great American industrialists of our day—a man who has rendered yeoman service to his country in this crisis—recently emphasized the grave dangers of “rightist reaction” in this Nation. All clear-thinking businessmen share his concern. Indeed, if such reaction should develop—if history were to repeat itself and we were to return to the so-called “normalcy” of the 1920’s—then it is certain that even though we shall have conquered our enemies on the battlefields abroad, we shall have yielded to the spirit of Fascism here at home.

I spent the better part of the past hour or so researching it and while the quote is brought up often, in varying contexts across the web and in print, I can't find a single footnote or annotation where someone cares to offer their reading of whom he is specifically referring to. His ambiguity in the speech itself makes me think it's either someone exceedingly obvious and would be readily apparent to any listener, or someone who was deliberately left unnamed because of their lack of general public name-notoriety.

My first inclination was the same as yours, that it would be Joseph Kennedy he's referring to, though alternatively I think he could have been referring to Dr. Donald Nelson. Nelson was a business leader (of Sears Roebuck) who did go on to serve as head of the War Production Board, which Roosevelt had heavily relied on in the years before this speech was given. (Edit: and, as I read more about it, was being slowly phased out of this position right around the time of the speech, so Roosevelt's willingness to show him a nod of appreciation while still leaving him unnamed would make some sense.) I cannot find any record of Nelson himself using the phrase "rightist reaction" publicly, and Roosevelt does seem to be borrowing that phrase directly from his said 'yeoman,' but the only person to whom the words "rightist reaction" are attached during this period in the public record that I can find are, of course, Roosevelt himself.

I know speculation is frowned upon on this subreddit, but I can't see any confirmation anywhere as to who he was referring to, so I've just given my best guess.

To follow up on /u/ewest's great answer, I'll offer another interpretation, that Roosevelt was referring to Charles E. Wilson, executive vice president of the War Production Board. New York Times coverage of Roosevelt's speech explicitly states:

"President Roosevelt hailed the recent warning, given by 'one of the great American industrialists' (believed to be Charles E. Wilson, executive vice chairman of the War Production Board), against 'rightist reaction,' and said that if such a reaction were to develop and the country returned to 'the so-called "normalcy" of the Twenties,' it would have yielded 'to the spirit of facism.'"

Wilson had been president of General Electric until 1942, when he assumed his position on the board at the request of president Roosevelt. Nicknamed "Electric Charlie" to distinguish him from the Charles E. Wilson who headed General Motors (and was appropriately nicknamed "Engine Charlie") he stayed in that role until August 1944, when a dispute with Nelson disrupted their working relationship to the breaking point.

Wilson was a firm conservative Democrat. In 1944, before his resignation from the War Production Board, he advocated that the United States should remain on a war footing and continue wartime levels of spending even after the end of fighting in order to avoid a national recession. "Instead of looking to disarmament and unpreparedness as a safeguard against war, a thoroughly discredited doctrine," he said, "let us try the opposite: full preparedness according to a continuing plan."

Partially because of that point of view, President Truman thought Wilson was the ideal candidate to head the new Office of Civil Defense Management when it was created in 1950 following the Soviet Union's development of atomic weapons.