Did they try to culture the bacteria from a mucous sample? That is extremely important, and it'll tell you what antibiotic will work on it. Ya gotta know what you're fighting. And, what if it's some sort of fungal infection? If it's a fungal infection, antibiotics will not work on it!
My only additional comment would be to refer you to the force feeding/hydration article in our Health Pages (bottom right of the screen). Has your vet given you a liquid diet for your cat, because if not it's very important that you feed your cat at home. IV fluids are fine, but won't do for long. I've had cats with stuffy noses that I fed at home for quite a bit of time, at it was the difference between life and death. As long as he'll swallow, you can feed and hydrate him. Please feel free to pm me if you want more details than are in the article.
Also, perhaps a second opinion is in order? If you are not 100% satisfied that your vet is as knowledgable and communicative as you need, then by all means, seek out another. Maybe a good sized animal hospital with a staff of multiple vets would be a good idea. I swear by places like that, when it's a serious situation.
Also (ok, maybe this is more than one additional comment...!) there are some things you can do in the meantime to try to lessen the symptom of the stuffy nose. I have used a pediatric OTC product called Pediasure that is a little plug in device that gives off vapors of nice stuff like menthol and lavendar - it definitely eases the congestion and breathing. Put your cat down in the bathroom since the vapors are more concentrated in a small room (also you can run the shower hot at the same time and let your cat breathe the steam). Doing this maybe once a day or so should help.
In a pinch there are ways to suction your cats nose so that he has a period of time to breathe easier and maybe smell a little. You can ask your vet about the little suction device that you can buy.
BTW, are there any other symptoms going on, like discharge from the eyes, diarrhea, drooling - anything like that?
Thanks for your advise. They just put her on Baytril and Prednisone. She is trying to drink a bit on her own but we are syringe feeding her. We are trying to expose her to the hot showers as much as we can.
Right now it sounds like tons of phlegm in her sinus cavity. The vet has flushed it and got back the cytology which shows a bacterial infection. We are hoping that after a bit more time on this course of antibiotics she will improve enough to eat on her own.