Let's say your opponent has 3 Pokémon in play. An active Gardevoir, a Benched Claydol and a benched Ralts. It's your turn, and you attack with Draco Meteor. You flip a coin for Gardevoir; Heads, so it gets 50 damage. Then you flip a coin for Claydol; Tails, so it gets nothing. Then you flip a coin for Ralts; Heads, so it gets 50 damage.
You flip a coin for each pokémon individually, and if it's heads, you do 50 damage to that Pokémon.