I have done a lot of flying with my LO, with much success (little crying, that is). We went on our first flight when he was 8 weeks old, and he's been on many flights since, so please let me know if you have any other questions.
Here are some tips that come to my mind immediately:
For an infant, I always tried to have him nurse/take milk from a bottle during take-off and landing. This does help ears, and it helps better than a pacifier, because it is the swallowing that helps their ears pop, not necessarily the sucking.
Bring plenty of quiet toys for the ride, especially books if your son likes you to read to him. I find a portable DVD player to be invaluable - but I hold off on using it until he is bored with all his other toys.
I recommend taking the car seat, if at all possible. If you bought him a seat on the flight, I'm sure you would. But even if you didn't, if there are any empty seats on the flight, if you ask the flight attendants/gate agents they will often move you to a seat where there is an empty seat next to it. Then you can use the car seat on the plane, and it is much more likely that your son will sleep/be comfortable if he has his seat. If there aren't any empty seats on the plane, then you will just have to gate-check the seat, which isn't hard.
At security, just be very organized. Although you can't take liquids/gels through security in general, you can take baby food, liquid formula, and breastmilk. Have any bottles and/or baby food in a separate container so that you can tell the TSA officer that you have it and they will inspect it. Be prepared to take the baby out of the stroller, fold the stroller and put it through the x-ray machine, because you will have to do that.
Give yourself lots of time to get through, because it will take longer to get everything back together after security, and also because you want to change your son's diaper just before you get on the plane - most plane restrooms don't have changing tables in them (there are a few exceptions, but not many) and in that case, your only option once you are on the plane is to change the baby on your lap! And the people in the seat next to you just love this ;)
If you fly alot, you know this, but most flights don't serve food anymore, so be sure to take enough food with you so he doesn't get hungry on the plane!
That's all I can think of for now - good luck!