We have awful awful flies thanks to the cow pasture next to the house. Maggots, as icky nasty as they are, are part of any animal around here b/c the poop has to go somewhere so it's either under the hutches, or where ever else it would go. The *only* time I have had issues with maggots was in an unhealthy rabbit. I bought one that was overweight (Grumpy advised against it, I didn't quite fully understand why it was an issue) and she couldn't clean herself properly. I noticed a bit of a funky smell, didn't think much of it. Then I realized the flies were congregating more around her. Hmmmmm... looked under her and there was a wad of gunk clogging her vent area. By far the nastiest thing I have every encountered with rabbits, maybe even animals in general. Anyway, I tried cleaning her up, but really didn't have a clue what I was doing. The next day she was wide eyed and twitching, with flies all around her. Yup - maggots in her vent area. I get queasy just thinking about it. I panicked a bit and culled her right then and there. She looked absolutely miserable so it was more out of mercy than anything.
All that to say this: for a normal, healthy rabbit it's not an issue. All the others have been fine.