Having had rabbits for 12 years, I have gone through that a few times. It is often caused by one of the same bacteria that causes Snuffles, the dread disease in rabbits. Pasteurella mutocida is the one that rabbit owners tend to fear the most, but Bordatella bronchiseptica, Staphyloccoccus aureas, Pseudomonas aeruginosa, and other bacteria as well. Pasteurella and Bordatella are the ones I have dealt with most, both in my rabbits and in the rabbits of others. Pasteurella can cause many problems; snuffles symtoms, eye infections (conjunctivitis), abscesses (internal and external), wry neck (torticollis), mastitis (infection of the mammary glands), pyometra (infection of the uterus), orchitis (infection of the testicals), and septicemia (infection of the blood stream, which can cause a lot of different problems). Bordatella can cause many of the same problems.
Depending on the bacteria causing it, it may be almost impossible to cure. Pasteurella is especially well known for being very hard to cure. Many of the antibiotics used only kill off the bacteria from certain parts of the body, but do not reach it all. This means, at best, the rabbit remains a carrier of the disease. At worst, the infection will return, possibly worse than before.
It is extremely important that you get a full culture done, if your vet has not already done one. A culture tells the vet what species (and possibly subspecies) of bacteria is infecting the eye, and they can test the bacteria's sensitivity to different antibiotics. It may be possible that you are dealing with a straing of the bacteria that is resistant to the antibiotic that is being used. In that case, it is essential to know that so you can switch to a different antibiotic before it is too late.
Keeping your rabbit hydrated is vital. If she is not drinking on her own, ask your vet how to force water into her. You can use a plastic syringe without the needle to give her water. Dehydration will worsen her condition, lessen her ability to fight off infection, and will cause her to die much faster. Keeping something in the digestive system at all times is important, too. Healthy rabbits never have empty intestines. There is always food, in some stage of digestion, in there. This keeps the gastrointestinal tract moving smoothly and keeps it healthy. Without anything in there, it can lead to gastrointestinal stasis, which is where the gut stops moving. This can lead to the "bad" bacteria taking over the "good" bacteria in numbers, and causing an entirely new, deadly, problem.
Good luck, and I hope your baby makes it.