Hi Elise,
Staph is a bacteria that freqently hangs around in CF'ers lungs. MRSA is Staph that is resistant to drugs in the penicillin drug class. So if someone has MRSA, they can no longer use Penicillin which used to kill staph pretty easily. MRSA can become sensitive again and then it becomes ordinary staph again. Sometimes Staph/Mrsa disappears on it's own (this has happened to me).
One of the reasons they don't treat it, is just because it is present in the lungs, doesn't mean that it's causing any active infection. And if they treat it, it tends to come back anyway. So that was a waste of using an antibiotic for when you might really need it. And each time you use an antibiotic, it makes a bacteria slightly stronger and harder to treat in the future. I am sure this is what your doctor meant.
There is also a belief that Staph sometimes helps control Pseudomonas because it doesn't give Pseudomonas as much room to take hold.
Just to make you feel better... so you know it's possible: A few years ago I had MRSA that became Staph, now nothing. This last time, I didn't take antibiotics, but I did go on H.S. and added some supplements.