Well, its got two uses really - one for removing/hiding rabbut smells. Its strong smell is an advantage here if you want to make a hutch smell neutral for bonding etc.
Vinegar is also good for removing wee stains where rabbits have sprayed or its collected in litter trays. In this case it might need a good soaking dependng on how bad the stain is. I leave a layer of vinegar in my litter trays for a few minutes then rinse them out. You can either let the vinegar dry off or rinse it all down afterwards.
For general cleaning I wouldn't use vnegar - use either a specialist cleaner like Virkon or a weak diluted bleach solution.