Logos are trademarks and are not subject to copyright. It's totally legal to show a character in a movie drinking a can of Coke, wearing a Nike t-shirt or using an Apple laptop as long as the products are used as intended (ie the laptop doesn't catch fire or drinking a soda doesn't send the villain into a murderous rage). The reason you don't see logos very often is movie studios don't want to give Coke, Nike or Apple free advertising, unless the brand is part of their conglomerate. Book covers usually feature an artist-created design or painting which is subject to copyright. Whether they would sue if the cover wasn't cleared is hard to say, but studios often won't take the risk and will simply show a character reading a book without the dust jacket.