Depends entirely on the route.
If it's one or two people going from NYC to SF, I think it's incredibly difficult to justify flying private. The costs are high, you're not going to save much time (especially if you're using an aircraft with insufficient range that has to make fuel stops), and there's plenty of commercial service.
On the other hand, flying a dozen people from NYC to SF is another story, as the cost difference vs. commercial narrows significantly.
Based on my experience, the best uses for NetJets or other offerings is getting to places that are not well-served by commercial airlines or for moving a decent-sized group of people who all need to be in the same place at the same time. I have colleagues who routinely have to visit companies in the middle of nowhere, and NetJets lets them fly to a municipal airport that can save hours of driving.
But using NetJets to send one or two people to a place like Boston or Chicago that has multiple flights every hour is just ridiculous.
And you're right about the comfort -- it's not like you're going to be relaxing in a king-sized bed at 35,000 feet with servants to dip your strawberries in chocolate. I remember being in a Falcon 900EX flying HPN-OAK earlier this year and wishing I had been able to fly UA JFK-SFO in F instead so I could at least lay down.