Dude I have the SAME problem right now and am due to fly on Sunday. I had a case of bronchitis a couple weeks back and also had a lot of sinus congestion. I still have a lot of fluid in my right middle ear and am mostly deaf as a result. Early on the pressure was so great it was causing significant pain, but that has subsided so I hope it means the fluid is slowly draining.
I flew once before when I was in this situation and the pressure changes hurt like HELL. There is also the possibility of rupturing an eardrum if the pressure gets too great. In that case the fluid will actually drain out your ear canal and the pain will subside. And your eardrum does recover from this, I guess.
I have been looking around online at ways to fix this problem and there seems to be only two options: wait it out and let it drain naturally (which can actually take MONTHS in some cases), or have an ENT doctor actually pierce your eardrum and put a tube in there so it can drain. They sometimes do the latter for young children as their eustachian tubes are especially susceptible to not draining properly.
A dr told me to take Claritin-D but it's hard to say if it's working or not.