Conventional wisdom is that you should either empty your pen completely before flying, or keep it completely full and carry it always nib up. Filling a pen minimizes the volume of air left in the ink chamber, air that can expand and force ink out the nib in the event of changes in temperature or outside air pressure. Blotting the nib and feed with a tissue right before takeoff will also help by removing ink from the feed channel, where it could be expelled by the expanding air in the ink chamber.
Paradoxically, we have found that earlier pens with very simple feeds are among the best to fly with. Fins and other devices that retain ink in the feed sometimes backfire here, preventing the feed channel from being completely cleared of ink before takeoff.
We have found breather tubes similarly ineffective at preventing leakage during flight. Protruding down into the ink, they instead seem to insure that there is a pressure relief channel full of ink no matter how well you blot the nib and feed.
Conclusion: follow the conventional wisdom, but uncap your pen and watch it carefully with tissue in hand until the plane reaches cruising altitude if you want to play it safe.