I don’t know if azithromycin is suitable for long-term treatment. It is the same type of antibiotic as Baytril (enrofloxacine), but it has some additional action on anaerobic bacteria (bacteria that don’t need oxygen) so it could potentially be more useful in treating bunny URIs.
I think you could ask your vet why Ollie was put on Baytril instead of azithromycin, if you felt the azitromycin was more effective. It could be the (known) risk of azithromycin killing off such a lot of the good GI bacteria that really bad bacteria (f ex clostridium difficile) can “hi-jack” and colonize the gut, which can be lethal, because those bad bacteria produce very harmful toxins. This can happen with erytromycin too, but it seems the risk is lower-I’m not at all sure though. Baytril is generally first choice abx for many bunny ailments caused by bacteria.
Here’s a little bit of info from the House Rabbit Society about appropriate use of antibiotics in rabbits:
http://www.rabbit.org/health/antibiotics.html