Up to 4.18 Tom did an awful lot. Top Pilot, Fathered an entire advanced Civilization, went on Away missions, helped with Engineering, was the nurse, was in the Holodeck many, many episodes.
After this point, from what I know, he continues in all these aspects, plus builds the Delta Flyer.
I don't think he was underused at all
The only thing more you could do with him was make him First Officer, and that didn't help Chakotay's character much