i had same problem!
i know how you feel, i started flying in Dec last year and was sick thru the whole of Dec, and most of January! i had worked for an airline before and never had any of these problems... so i dont know what changed, but i know it was not a pleasant experience AT ALL having to try and work on a plane with a red stuffy nose, blocked ears etc. ive never been one to get sick much so it was a real pain in the neck. i had to go sick in the middle of a 3 day trip bcos my ears had 'just' managed to equalise on most of the decents we did but finally they just blocked completely and i was terrified of bursting my eardrums- it ended up being a middle ear infection- i wasnt impressed.
definitely go to your doctor if youve actually got an infection bcos you probably need antibiotics, but heres a couple of remedies that have helped me!
hope this isnt too long but this info helped me, & once i really understood why it was happening (thanks to my Doctor) then i was able to try and 'prevent' it as much as possible. basically bcos your body is adjusting to the flying environment, lack of humidity etc, your sinuses especially can become 'dried out' - when they become dried out they are particularly susceptible to bacteria and infection and therefore you end up developing colds/ear probs.
the doctor i went to gave me strong antibiotics for the infection, but also told me if i could, it would be really helpful to go and spend a few hours at the beach so i could inhale the salt water, as the salty water would kind of 'lubricate' my sinuses etc. so i went that nite (it was december so it was warm at least! : ) and when i got there i was so stuffy in the nose that i couldnt smell a thing- within an hour of sitting there i could smell the salty air and seaweed! and my nose was unblocked too! it worked! he also suggested that if i was working long days in the air, to stop for a minute or so & inhale hot water in a cup with salt in it thoughout the day- the next best thing to salty sea air!
lastly something that you can use ongoing which has been FANTASTIC for me and 'touch wood' i havent been sick again like back in Dec- is a product called FESS. its just a saline spray, so no chemicals involved, and the one i bought has tea tree oil in it also which i think is good to have bcos it has lots of natural healing properties. you just buy it over the counter at the chemist and its a nasal spray. it basically just lubricates your sinuses and you spray it twice before a flight and then thoughout the flight as well. i dont use it every time i fly anymore as i guess my body has finally started aclimatising (wrong spelling?) but i do use it on longer days ie. 6hrs or more of actual flying time. its great and has worked a treat for me, i just keep it handy in my bag.
hope these help, of course there are antihistamines etc that people use and i have used them too, but i really did find that the FESS has helped me the most. once you can get rid of the infection you now have - which may unfortunately mean taking some time off sick (i had to have 12 days off to fully recover) then you can work at preventing it happening again. i know its difficult to take time off work when you have only just started but it really is important you dont fly with ear probs as im sure you know- its just not worth it- and a letter from your Doctor saying youve got ears issues bcos of a cold is more than enough- no airline can argue with that. i actually found that crewing were great and just said 'no problem- get well soon'.
hope this helps, take care and happy healthy flying!
andie74