"Do you want to go to the bathroom?"
Translation:Chceš jít na záchod?
Because that is the preposition that is used inn this case, that's all. Like the choices for in, at, to in English, one has to learn all the usage by heart. Jít na záchod means to go to use the toilet. Jít do koupelny means to go inside the bathroom (for whatever reason). Jít na koupelny does not exist. Unless it is a box and you can actually go on the top of the box.