Remember when Travelin' Dad and I touted scheduling flights during your infant's nap time? Sometimes TJ would fall asleep for a blissful 25 minutes on the plane, and we could both breathe a sigh of relief. Well, I'm sorry to tell you that there comes a time when your toddler will likely refuse to nap on an airplane. I've done an informal poll with my girlfriends, and somewhere around 18-24 months, the world of flying on a plane just becomes too interesting for kids to sleep through.
TD and I learned this lesson the hard way, having to make it through two flights during TJ's usual naptime, in which he refused to sleep. Read: he was cranky, whiny, and required constant stimulation/attention. So, after your child reaches this magical age, I would actually recommend flying in the mornings. Most toddlers take one nap a day, around noon or one. If you fly in the morning, your child will generally be in a good mood and not tired. Once you reach your destination, you can still try the afternoon nap. Or, if your toddler is too excited about their new digs (as TJ often is) to sleep, at least you can go out and explore your new surroundings. Better to deal with the effects of a missed nap while exploring a new city than it is while trapped in a metal tube at 30,000 feet.