For me that is not natural behavior.
That may be so for you, but for most MB users, especially those who have been using it for quite some time, changing it now would cause lots of confusion.
Ticking -enables- or includes the ticked object in the process. It's the same as -selecting- a file to be included in a process. In Windows Explorer do you want to take action on the files that are -un-selected? No, you want the action to take place with the selected files. And that's what the tick does in your example - it is indicating an episode that hasn't been listened to.