In addition to the points made by the other comments, I'd also add that "thus more stops" doesn't necessarily follow. Amtrak tends to be the subject of a lot of stupid politics, with the routes and stops determined more by what wins votes than what makes sense. As a result, a lot of Amtrak routes stop extremely frequently in pretty small towns.

As an example, the Amtrak train that runs between Washington DC and Boston (serving NYC along the way, and continuing on to Norfolk, VA) stops not only at DC's main train station, but also at New Carrollton, MD and Alexandria, VA, which are not only quite close to DC, but actually on the DC Metro system, making these stops almost completely redundant.

I count no less than thirty two stops between Boston and DC. The trip is about 9.5 hours long, so that's an average of one stop every 18 minutes.

The NYC->Chicago trip isn't quite as bad, but still has 19 stops in between. Along the way, it stops in such bustling metropolises as Elkhart, IN (population 51,152) and Sandusky, OH (population 25,493).