I'm not judging LouLou here-you know I love you L!!! Everyone has to make the decision that their doc and them feels is best.
But just to show you the flip side, I am not on TOBI and my doctor spent a year with me, weaning me off it before my pregnancy. Basically the jury is still out on how much gets to the fetus. Its one of those situations where there is no proven evidence that says it is that dangerous, but there is also no proven evidence that says that it is safe. My docs personal feeling is, do not take it since it is proven that the medicine tobramycin which TOBI comes from can cause hearing related birth defects. TOBI is that med, its just expressed in a different way, through the lungs so maybe there is not as big a danger to the baby. But I don't want to risk that 'maybe'. And since I have a good relationship with my doc and pretty much take faith in what she says b/c she's shown herself to be very level headed with me, I'm going with her on this one.
The other thing is, she may feel that I really don't need it. For someone else, they may need it. There's also the risk/benefit ratio for a cf mom to consider. Healthy mom-healthy baby. So if the mom feels she needs it to stay healthy, then she needs to make that decision.
Since you don't have to worry about that, and its not your health at risk here, I'd have him do his nebs in a well-ventilated room in the house, far away from where you will be at the time. Maybe stick an airpurifier in the room with him. Play it safe. You never know. Then you can say at least that you took all the precautions you could at the time. That's just my opinion.