DD was having some breathing trouble before our last trip - I didn't really think she was that bad, and the day we were supposed to leave (7pm flight) she seemed to get worse - so I took her to the Dr. at 2pm - turned out she was having more trouble breathing than I realized and Dr. put DD on nebs (our first time ever, so I was clueless) but cleared us to go - with nebs every 4 hours. Luckily, when I was in the med supply store freakign out b/c I was so overwhelmed, the guy mentioned they had portable nebulizers. It cost 150 more than was covered by insurance (yikes!) but it was a life saver b/c we could fit it in our diaper bag, take it to the parks and it ran on batteries. We ended up having to go to the ER a few days later b/c she wasn't responding to the nebs as much as she should and they gave her a steriod - again - b/c she was so little (8 months), said she was fine to go back to the parks b/c she wasn't walking, running, getting over excited, etc - just being held and riding in the stroller. SHe cleared right up after the steriod and we were able to enjoy the rest of the trip!
Anyway - point is - if you haven't already, give your doctor a call and see what they recommend - they might surprise you and either clear you!
(As a side note, DD already had ear tubes, so no matter how much congestion she may have started with, we weren't going to have ear pain/pressure problems on the plane - had she not already had tubes, I may have cancelled.)