Well, my sense is that most vets don't see many rabbits and are therefore less experienced with, and more cautious in, treating them.
And it may be that there is less actual data available on the use of Revolution with rabbits than with cats and dogs, so he wants to be especially careful. For any medication, there's a risk/benefit issue, and you want to expose the patient to as little medication as possible.
And I would agree with that, but in my case, my rabbits have had fleas and/or mites a couple of times, so I feel the benefit of preventative treatment outweighs the small risk of whatever side effects are possible. And now my vet seems to agree with that.
As for dose, it goes by weight. So for my 3 lb bunny, I use the full kitten dose (I think the package says for under 5 lbs), but for my 8-9 lb bunny I use the next size larger.
What is the weight range for the vial he gave you? If it says for less than 5 lbs, you could use the whole thing, but if he weighs only 2 lbs, it might be adequate to use half of it. Then you'll have enough left over for a future dose.