The problem appears to be the old tracks (speed restrictions) and old signalling system which increases delays and lowers throughput.
EDIT: To use the route here as an example. According to google maps the distance is 83 miles on road, so probably around 80 miles for a train. This can easily be done within 45 min on a train. Have a look at the German cities of Cologne and Frankfurt. There's a high speed train running and I know some people commuting there. It's not nice either but a distance of 150 miles with <1hr commute each direction. The ticket costs ~$4,500 per year which includes free rides on all trains within Germany. There are 3 stops on the way and some people only commute half the way which makes it a 20-25 min commute for the same distance of Philipsburg to NYC.
This exists in France where some countryside TGV stations have become Parisian commute towns.
E.g. Angers-Paris (296km, 1h15 by TGV) - http://www.lepoint.fr/villes/tgv-boulot-saint-laud-25-10-201... (French)
For not much more than 8 hours at the office (depending on how far away from Penn it is) you'd be away from your house for more than 14 hours every day.
I really do not see the appeal of hyperloop in any situation involving high density land use, and I also do not see how it could work in locations without high density.
Difficulty would obvious vary quite a lot by city, and I imagine NYC is basically irreparable since you can't even get a line into it. But it would at least have potential for less dense locations.