I know this is an old thread, but my oldest turned 3 on his first trip (2009), and never questioned.
My kids were 9, 2, and 2 when we went in 2015...we were never questioned.
This year at 10, 3, and 3...I actually had more problems having to tell CMs what to charge us at character meals or telling the CM at the turnstile that the twins did, in fact, need to scan their magic bands). My kids are on the shorter side, though.
ETA: At 1900 PF, the server kept asking everyone's ages. Then she said it couldn't be 3 adults and 2 kids, walked off and we were charged wrong (less than we should have been). We really needed to leave as DH was feeling ill, so I didn't argue the bill. Maybe she was trying to give us pixie dust?