He was a captive to Vito's generosity. Tom was the most loyal because he wasn't a Corleone by blood. He came from nothing, which is why he could have never turned against the family. Vito probably did have some ulterior motives when taking Tom in, but they probably didn't go that far into the future.

I also think that Tom is Puzo's representation of Vito's generosity and kindness, that he would take in a non-Sicilian and raise him like his own. I think that it's perhaps Vito's strongest characterization and the one that sets him the most apart from his advisaries.

Michael and Tom have been discussed a lot recently, so I find it more interesting to focus on Tom/Vito.