I fly a lot and never have had an issue with my two Cross Century II cartridge/converter fountain pens the following:
1. Push the air out of the converter (pen, upside down, empty air until I see some ink in the nib).
2. I store my two Century II fountain pens inside a zip lock bag.
3. I put them into my carry on bag, below the seat in front of me, in the upright possition.

4. Once the plane levels off, I do take them out and use them. Never had an issue with them.
I have had an issue with needlepoint and rollerballs (disposable type). But never with my two trhustworthy fountain pens. I haven't tried pens that I can't release air from them. (Sac pens, pistons, or anything like that).