I popped an eardrum while flying several years ago---I truly felt like my brains were going to siphon out of my head! I didn't have a cold at the time, but I do suffer from various allergies, so while I felt fine, I wasn't.
Since then, I've been instructed to start taking sudafed, or another decongestant, about 24 hrs before a flight...no matter how well I feel. And continue dosing myself until the flight is over. Since then, no problems...except on the trip or two I didn't.
And I now add a decongestant to the scheme....ever since I found myself unexpectedly sitting behind a cat in a small first class cabin. My sneezing and coughing started about 15 minutes after boarding, luckily my seatmate had some claritin and my symptoms calmed a bit within an hour. Now I always make sure there's at least two floating around my bag....and take one the day prior to the trip, too.