This may seem like an obvious question but have you shown him that there is water in the bottle? The easiest way is to take him over to the bottle and very gently press his nose on it so a drip of water comes out onto his nose. He should soon get the idea. If you have already tried something similar then maybe try putting some of the milk formula that you have just weaned him off into the bottle until he gets used to using it. You could even try hand feeding him water from the bottle in the same manner that you used to bottle/syringe feed him before. If all this fails then you might just have to accept he’s not a rabbit that will drink from a water bottle and provide a water bowl.