The author's terrorism concerns are way overblown and the reasoning supporting them specious, but there is a more basic issue with hypersonic point-to-point transportation systems outside of the additional arguments related to current air travel, at least for vehicles designed to go suborbital/exoatmospheric:

Once we are talking about traveling to a destination and not simply going "straight" up and down, the costs, maintenance issues, safety requirements, development time, thermal management, mission management, guidance systems, etc., get within spitting distance of actually developing an orbital vehicle.

Future technology improvements and cost reductions cannot be ruled out, of course, but given the basic physics and what we know of the near future of aerospace technology, it seems a stretch (at least) to expect a profitable, safe point-to-point suborbital system to be a viable undertaking.

And once we are talking about orbital systems, where the cost and risk/reward equation at least seem to be more desirable and unrelated to point-to-point travel, the question of suborbital point-to-point fades into the background.