I had a similar experience twice this year.
In July, I had been diving in the Carribean, and didn't realize I was sick at all -however, I got really congested on my 2nd flight from MIA - LGA and I seriously thought my head was going to explode during the descent. My ears didn't clear up for a week. My ENT gave me some antibiotics and advised Sudafed and Afrin for future flights. I rearranged my work schedule to stop flying for a couple weeks, but I really thought it had to do with the diving - not the flying.
Then I came down with a cold in Chicago while on business in October. In light of the prior incident, I should have been smarter, but I decided to 1) fly home early, since I had already been away from home for a couple weeks and 2) balked at the $12 cost of Sudafed at ORD. Once again, big mistake. My ears were clogged up again, and I really felt like it took about 8 weeks to totally clear up. I feel my hearing is back to normal now, and now I definitely attribute the earlier incident to the flight as well.
Since then I have religiously been taking both Sudafed and a nasal OTC before flights - my ears have been ok so far. The physican's asst recommended I wear ear plugs, although I am not sure how that will help out and have yet to try that.
I am a little nervous about future incidents. My ENT has suggested potentially considering ear tubes - has anyone had any experience with those has adults?