The only reason they are in the movie is because Harrison Ford himself swore by them while he was working as a carpenter, prior to becoming a big time actor. He insisted that he wear them for the film as well. He apparently has really wide, flat feet or something, so they fit his feet well.
The fit and look of the Indy boots is definitely not for everyone though the look has become a bit fashionable nowadays. Keep in mind, they were originally orthopedic boots.