Our family has been on the Autotrain 4 times. Our kids are 8 years apart, so I've done it with a 18 month and 9 yo, 3 yo and 11 yo, 5 yo and 13 yo, and 6 yo and 14 yo.
They've all been wonderful trips. We went coach each time, except the last, when we upgraded to a sleeper. With young active children, there are advantages to coach, because there are lots of other children on the train, and my very active children are quick to make friends. (They assign people to what we call the "Families From Heck car"; the Mellow Boomer/Gen Xer car and the Uptight Greatest Generation (Quacker) Cars so you don't have to worry about your child disturbing people without kids.) Some of our tips are to arrive early and request the seat in the car with the plug; then they play movies on the laptop. Or bring a gameboy.
We get the 5:30 dinner reservation, and there are snacks available in the lounge once the train leaves.
They show a movie at 7 in the lunge. And by then it's time for a few bedtime stories and bedding down.
If we don't have the plug seat, we try to grab another set of unassigned seats so both people can stretch out.
Then when you get up in the am, before you know it you're there.
I bring lysol wipes for the toilet seats. And bottled water to sip in the middle of the night. And have been known to slip my active daughter (with legitimate allergies) "sleepy benedryl" at bedtime rather than the usual nondrowsy allegra.
When she was in the preschool age I also brought a few surprises to space out over the hours. For some reason she loved the "magic pen" books (they had them in the autotrain waiting room) the most.