I have two dogs and a house rabbit too who is never in a hutch. He is just loose in the house and has an open cage to potty, eat or rest in.. It is totally normal for a dog to want to chase anything that runs, but that doesn't mean you can't teach the dog that it is not ok to chase the bunny. Here's what I did and I would suggest you try: First, teach the dog a name or word for the bunny. So either use the rabbit's name or call him 'bunny' or whatever. Do that several times a day with you holding the bunny and letting the dog sniff him (with your protection for buns), until you are sure that the dog knows the word you are using. If the dog gets excited while sniffing (ears up, licking lips, overly alert looking) say, 'NO', stand up and turn your back with bunny away from the dog. That way the dog learns he can only get the reward of sniffing bunny when he is calm. During the same few days while you are teaching the dog the name for bunny and not to get worked up over it, also work really hard on teaching the dog what it means to 'leave it'.If you don't know how to do that, write back and either I or someone else here I'm sure can help. It is really useful for all kinds of situations.
Anyway, after the dog is really solid on leave it and knows the name for the bunny, Let them have short supervised visits out of the cage, assuming the dog isn't aggressive and isn't alerting to bunny anymore. Start with the dog on leash and allow him to sniff the bunny but if the bunny starts to run and he starts to chase, give the 'leave it' command and follow through so the dog doesn't scare the bunny. I would do this in a room or other enclosed space because bunnies are really hard to catch when they don't want to get caught! LOL If bunny can escape when he feels threatened, and dog isn't allowed to chase, they will both grow in trust of each other. Like you said, bunny will likely be wary but shouldn't be scared stiff. My dogs still occasionally harrass the bunny but he is pretty tolerant and hops into his cage when he's had enough. Usually he comes out again within a couple of minutes and he now seems to like to interact with the dogs, as long as he has a place to hide if he needs it when I'm not around.
I would recommend not having them loose and alone together, maybe ever, depending on the size difference between them. My dogs are 12 pounds or so and the bunny is nearly 7 pounds so even if they wanted to do him harm it wouldn't be too likely. If I had a 40 pound dog it might be another story. I recently brought another dog into our home for training and used the same method with her. She learned very quickly to 'leave it' with the rabbit and seemed to like to hang out with him.
I don't think it is unfixable. If your rabbit is anything like mine, he will have a short memory and as soon as the dog learns not to chase, bunny will be just fine. Good luck, remember 'safety first' for you, dog AND bunny, and let me know if you have any more questions.
