Are you sure it was just a Bendis thing and not also an editorial decision? A reason other media went trunkless was because the comic books went trunkless. With the trunks back I could see the movies going back to trunks.
Its not like there seems to be a Superman movie coming out anytime soon so by the time a Superman movie does come out people could well be expecting Superman to have red trunks. Especially if Superman is rebooted.