Was he just that well liked or did some people have a problem voting for him because he was breaking tradition?
Some people did have a problem voting for him in 1940. Republicans and anti-New Dealers in general used the third term argument against Roosevelt during the 1940 presidential campaign.
It was generally unsuccessful, as voter appeared to buy Roosevelt's counter-argument, which said that he had changed his mind after the outbreak of war. Secretary of Agriculture Henry Wallace (later vice president) broke the news of the third term in October 1939, declaring it was a necessity because of the war. White House press secretary Stephen Early infamously replied to Wallace's speech in San Francisco, saying, "It would have been kind and polite of the speaker to have consulted the victim before he spoke."
Roosevelt repeatedly denied questions from the White House press corps even after Democrats started a "draft Roosevelt" campaign during the national primaries. This allowed Roosevelt to dodge much of the rhetoric launched against him. A letter to the editor in the Oct. 27, 1940 issue of the New York Times has a pretty good chronology of events.
Wendell Wilkie, the Republican presidential candidate, tried hammering at Roosevelt on the third-term issue. Roosevelt said that the United States would be better off with an experienced president during wartime. A letter-writer to the Times on Oct. 17, 1940 puts Wilkie's counter-argument clearly:
"As Mr. Wilkie points out, if this argument were a determining one, it would be an even better argument for a fourth term, and better still for a fifth or life term. A president's alleged indispensability, on that basis, would increase with each term. And the same argument, indeed, could be made for a life term for every officeholder or for the holder of any position in business life."
Of the four presidential elections, where FDR was the Democratic Party's candidate, 1940 was the one where FDR had the smallest margin of victory. The breaking of the no third term tradition is the biggest reason for this decline.