The reasoning behind that ruling (beyond the spell text not calling out for separate rolls) is partial covered on page 196 of the phbCaliban, on the previous page there were links to Tweets that specifically say that Magic Missile is an exception to that PHB Errata. Magic Missile no matter how many missiles you have, you roll only 1d4+1 & add your Int bonus to each missile.
"If a spell or effect deals damage to more than one target at the same time, roll the damage once for all of them"
Magic missile is currently the only non standard aoe spell that deals "simultaneous" damage so it's often over looked. Obviously this begs the question of what about if all the missiles target the same creature. Well, the rules generally treat spells that possibly have multi targets as if they always do but there's definitely wiggle there.