It’s actually very possible to miss the message of Bioshock. Andrew Ryan built the perfect city and Atlas ruined it. Andrew Ryan cast him out, but Atlas brought the player character as his final ultimate weapon. You eventually rebel, saving the capitalist Utopia.
I have seen people who abided by this interpretation. Any art with any level of subtlety can be misinterpreted. It’s inherently subjective and depends on the viewer’s personal biases.