In the case of "THRESHOLD", it's not all on Tom. Janeway let that happen, too. Chakotay decided to leavevthem on that planet (per his log entry), but she obviously outranked him... both as a captain and the kids' mom. She could have had them brought aboard.Trip was ready to be, but it didn't work out. I think O'Brien was a good father. Dr. M'Benga did his best as a father and seeing your kid become Pure Consciousness is kind of like them graduating, I guess. Tom Paris may have been a decent father to one child, but also abandoned his salamander babies, so.. you have to take that into account. Can't say if McCoy was a good father or not.
In fact, I'd say it's more on her than Tom.