I know way too much about ear pain on planes, not because my child has problems with it, but because I do. I have Meniere's, and I have to guard very carefully against ear problems when flying. The most effective combination that I have found is a preventative dose of a decongestant that is mixed with Guiafenesin, and then also a shot of a prescription steriod nasal spray. Of course, that'a bit much for the average child.
The only way that an antihistamine will help w/ ear pain is by making the child fall asleep so she won't feel it. What helps with ear pain (which is really sinus pressure) is a decongestant. If a ped. is recommending Benadryl to prevent ear pain, then he/she needs to specify the formula that contains pseudoephedrine. Here is a chart from the mfr., note that the only 2 of the six children's formulas are effective for sinus pressure:
http://www.benadrylusa.com/benadryl.asp?sec=3&page=50&from=3 Pseudoephedrine (aka Sudafed) will help with ear pressure, but it is a stimulant, and tends to disturb sleep and sometimes will cause nightmares. This effect will be less noticable if it is mixed with an antihistamine.
Lots of peds. think it's best to give children something to make them sleep while travelling; a sleepy child is less likely to be anxious and afraid of a strange situation, and the bonus is that not dealing with meltdowns from anxious children makes the trip easier for the grownups, too. However, I think that if the goal is to make a child less anxious, a better choice might be Children's Dramamine, which will help with nausea, too. (The active ingredient in that is also an antihistamine, but a different one; Benadryl is diphenhydramine; Dramamine is dimenhydrinate.) Dramamine does NOT make my son hyper; it does in fact relax him. He had reflux when he was younger, and tended to get airsick, so I used it often.
If you are worried about ear pain but want to avoid medications, I recommend Earplanes if your child will tolerate having plugs in his ears (mine never would), or having a sippy cup or sports bottle of water handy for takeoff and landing; the act of swallowing will help relieve the pressure. If a child does get ear pain and swallowing does not help, ask the FA for "cups for his ears"; they all know what to get for you. Take the cups they bring for you, turn them upside down to make sure no hot water drips, then fit them over the child's ears like muffs; a steam chamber will form over the ear, and the moist heat will relax the eardrum and ease the pain.
Regarding airsickess: I would advise NOT giving any young child dairy within two hours of a flight or during a flight, especially if that child has not flown before. Stick with water or clear juices; they are less likely to come back up if a child feels queasy, and much less foul-smelling if the worst does happen. BTW, always carry spare clothing for the child *AND* a change for the adult if you don't know if a child is prone to airsickness. Little kids can almost never manage using an airsickness bag; they need a bucket or large cup, something with rigid sides that can be quickly grabbed and moved into position. They tend to give no warning before getting sick, but will turn to you instinctively; if your child is prone to this, you are very likely to end up weaing the worst of it.
BTW, the most common time for a child to get airsick is right after landing, as the plane taxis to the gate; watch them carefully at that point.
Does anyonehave some good tips on flying with the two kids? We have a morning flight 8:55 AM. The 2 yro has a seat and we will be holding the 9 month old. I will make sure that the baby has a bottle during take off but what about the 2 yro? 
