You need to be careful with some abx. TOBI, while it's usually very well tolerated, has side effects that are irreversible. These include hearing loss and dizziness. Aerosolized TOBI has less chances of causing these problems, but it can happen. I was on aerosolized TOBI and IV TOBI for about a month once before when I started noticing that I felt like I was in a tunnel all the time. It messed with my hearing so we stopped it right away. This feeling did subside, however I believe whatever the TOBI did to my hearing was minimal enough for me to get used to and no longer notice. I don't think it resolved itself after stopping the TOBI. I don't mean to scare you, but I've met CFers who ended up needing cochlear implants after long term use of TOBI. I don't know if that is more due to IV or aerosolized or what the deal with it was. Since your son is young, though, I think you should know about the hearing loss/dizziness because it might be something your little one doesn't notice right away or wouldn't think to mention to you. With long term use of TOBI, I would suggest seeing your pediatrician and getting a baseline hearing test and then follow ups, just to make sure things aren't changing with out realizing it. I have to do this now every time I go on other meds that have the same possible side effects as TOBI.
I've been on Cipro and Bactrum for VERY LONG periods of time as well and they never really caused me problems. If anything, long term use got me more used to the side effects of those drugs, the most prominent one being nausea.
As far as alternative/natural meds, my mom once took me to an herbalist. At the time, our main concern was my digestive issues. This herbalist concocted a powder which I know contained garlic and dried pineapple. It contained several other herbs that I had never heard of. I took one spoonful of it mixed in juice anytime I had CF belly ache and it took the pain away. It tasted horrible and my CF doc never believed my mom and I when we told him it helped with the actual aches but I swore by it for years. I've also found benefits in taking cinnamon to help control blood sugar. I'm sorry I don't have anything really definite to recommend to you regarding natural medicines, but I believe that natural remedies are worth a shot. I've had some good experiences and I know others on this site have as well.
Good luck to you both!