E. cuniculi and an inner/middle ear infection would be the most common causes. But because it can sometimes be difficult to determine which one, until scans or blood tests confirm one or the other, many rabbit vets will start off treating for both with panacur(fenbendazole) for the EC, an antibiotic like baytril for possible ear infection, and meloxicam to reduce inflammation(higher dosage range).
http://wabbitwiki.com/wiki/Encephalitozoon_cuniculi
https://www.gwexotics.com/wp-conten...-E-cuniculi-infection-in-domestic-rabbits.pdf
Medirabbit (inner ear infection in rabbits)
If an ear infection is looking to be the cause, I would consider azithromycin over baytril(most commonly prescribed to rabbits). Infections can be difficult to clear up in rabbits, and this antibiotic seems to be an effective one(depending on the bacteria involved), and seems to work quickly. I've used it for a stubborn infection with some of my rabbits, and it cleared it up, with a reduction of symptoms in just a few days. Just can have a risk of severe digestive upset for some rabbits(in which case it shouldn't be used), or may start off causing some abdominal cramping that will usually subside after a few days, so something to be aware of especially if there is a resulting lack of appetite.
When the neurological symptoms are really severe, sometimes corticosteroids will be used instead of the meloxicam initially, just to get the inflammation under control quickly. But because of it's affect on the immune system, this is usually used as a last resort.
Medirabbit (corticosteroid use in rabbits)
Some other, or less common causes for ataxia, would be head trauma, tumor, toxoplasmosis(particularly for rabbits around cats), toxins, heat stroke, floppy rabbit syndrome(usually resolves in a week with supportive care), nematodiasis(for rabbits exposed to wild animal excrement), and for very young baby rabbits born with the issue(usually don't survive a couple weeks) it can be from vit. A toxicity during the mom's pregnancy. Even though your rabbit isn't showing signs of head tilt, the causes of head tilt and ataxia are going to be essentially the same.
http://www.bio.miami.edu/hare/tilt.html
http://wabbitwiki.com/wiki/Head_tilt
http://www.medirabbit.com/EN/Neurology/Toxoplasm/Toxo_rab_en.pdf
As for care, setting up towel rolls and supportive padded siding can sometimes be helpful, but that will depend on the extent of the illness and exactly how it's manifesting.
Info on caring for a disabled rabbit.
http://www.disabledrabbits.com/