BabyEagle's first flight was when he was 3 months old in a C172. He sat in the back with his mother and basically slept during the 20 minute flight.
Second time was when he was 9 months old, he stayed awake the whole time wide eyed.
Third time was yesterday (21 months): he sat in front on mother's lap and even held the yoke during cruise, pointing out at clouds oohing and aahing.
Regarding your questions I suppose it depends on the length of the flight: if it were more than 20 minutes I would consider ear protection.
In climbs and descents I have not exceeded 500fpm: make sure he doesn't have a cold. If he does experience sore ears he'll start crying and that will/should automatically clear his ears.
Boredom shouldn't be an issue: all the small kids I've taken flying after a while haven fallen asleep.
BabyEagle spent the rest of yesterday afternoon saying "aero - aero" and wanted to go back to the airport.
AE.
Please note, I'm not a doctor and the above is just my personal experience with my son.