No, I don't find it confusing. I think the game would be a lot more confusing and time consuming to play if you had to pair up opposites because you would have to think twice for every individual step of a puzzle. By having equals attract, the game plays faster because you only need to come up with a solution and execute the plan, no need to convert your abstract thoughts into something that a lot of players would accidentally get wrong even when they know what to do. It would pretty much turn the game into a very long Stroop Test
I also think the physics engine and many puzzle layouts would not work with actual magnets. There are several puzzles in the game that requires you to stack three magnets on top of each other. This would not really work for the cubes, Well, they could model actual poles on the cubes but that would just be awful to play. Players would have to be extremely precise in their handling of physics objects and they would be at mercy of finicky any crazy physics bugs.
I'm calling "representative realism" on this game. You are playing a character that manipulates magnetic forces with advanced equipment in stressful situations. To make the control scheme capable of delivering this kind of action and focus the gameplay on problem solving rather than mastering a convoluted and finicky physics engine, the visual representations of the magnets are simplified so that you as a player can focus solely on intention, while your character does the actual handling of the magnets. You could always imagine that when you make two equally coloured cubes smash together, your character has actually aligned the north and south poles to make the cubes attract.
THE GAME IS SUPPOSED TO PLAY LIKE YOU'RE A MASTER MANIPULATOR OF MAGNETISM. Compare this to Guitar Hero/Rock Band where your character is a skilled musician who is able to play anything, it is not your job as a player to get into the finer points of playing an instrument but rather just act out the rock star fantasy. An exact opposite of this philosophy would be Surgeon Simulator 2013 in which you are playing a (supposedly) educated surgeon, but the game is not built around delivering the illusion of controlling a skilled avatar but is mostly focused on you as the player manipulating the very fine movements of the avatar's hand (to the point of hilarious absurdity).
Alright, for me it's the absolute opposite. I have to think twice cause I automatically assume that same poles would reject each other so I have to unlearn that while I'm playing it. I'm getting used to it but I still mix it up sometimes. For me it would have been more intuitive if it worked the other way round.
Edit: I see what you mean, though when you say it would break a few puzzles with multiple magnets which you can put together to build a stronger magnet so I guess it was a necessary design choice.