it's been the trend ever since the 1989 Batman movie, at least there it was portrayed as "body armor", but it soon morphed into every superhero suit being padded muscle suits, even Superman's who doesn't need body armor.
truth is real muscles don't show through clothing/spandex they way we have become used to seeing them drawn in the comics. Affleck and Cavill are both in shape (especially Cavill) but to drape them in plain spandex/cloth would take away the bigger than life comic book appeal.
the funniest one is the Night Owl suit in Watchmen, Night Owl is supposed to be a little fat and out of shape, and far removed from his crime fighting career, and Snyder has him looking like Batman in that movie.
I think it went even further back than Batman 1989. I remember in the first Superman movie with Chris Reeves, they had multiple "padded" suits to make him look bigger. Some suits were made to make him look more muscular while standing, another for flying, etc.. Reeves did bulk up for later movies, but I think for Superman I and II, he was still a pretty lean guy.