There are a lot of factors.
- There are about double that number of trains if you count the Regional (which you should) so ~hourly trains.
- A lot of people still fly. Especially if you live in Boston proper, flying means you can easily make a morning meeting without flying down the night before (which people with families etc. may prefer not to do)
- Especially if you're south/west of Boston or in New York's Connecticut suburbs, it's probably cheaper/faster to just drive, something I really try to avoid when it comes to NYC but nonetheless for me taking Amtrak actually involves me driving for an hour in the wrong direction/