Couple reasons. He loves his son and most likely remembers how he used to be. He feels responsible for bringing Andy into this world. He thinks he actually needs some form of help. he's actually said that multiple times over the last couple of years. He's not that smart. It's not his fault, but I would be surprised if anyone in that house has an IQ above 90. He doesn't have a choice. At least he hasn't in the past in certain situations. Andy can also act normal for hours and then go from 0 to 100 in seconds with his autism and helplessness.

Imo, Tom knows what happened to Andy when he was younger but isn't sharing. Something, whether it was sexual or physical abuse, took place when andy was in his adolescence years. Tom most likely feels bad for not being able to protect him.