Given these all-too-real scenarios, you can understand why you don't need to be an anti-government free market fanatic to wish that politicians and the transportation sector could get their act together.

Still, we all know that's never going to happen. At every level, the government will never give up its iron grip on transportation. And politicians will never risk suffering the outrage of voters that would appear every time fares or tolls rise, or when commuter systems fail, without containing the potential fallout on Election Day.

Besides, some of the best urban planners in the world are arguing that major new projects aren't needed anyway, we just need better management. That's a key argument behind the "no new roads" push by groups like Strong Towns, who point out that infrastructure building is too often planned by non-local powers, who don't consider a given city's needs or how those projects will be maintained long term.

So where does that leave us? Is there an example that exists of a mass transit system that is both well-managed and financed, and where the commuters come first and politics last?

It turns out there is—and it's not in Never-Never Land. In fact, it's happening in the largest extended metropolitan area in the world: Tokyo.

In Japan's Tokaido megalopolis, with its population of about 38 million people, the large network of commuter and longer haul passenger trains in Japan have become the envy of the world.

For the last 30 years they've been running almost free of real delays, have never had a fatal accident in that time, and they actually run on a profit. They're even clean! And the secret to that success is a nice combination of free market advantages with realistic "light touch" government oversight.

You see, the commuter rails in Tokyo have been privately run for these last 30 years... sort of. In 1987, the government created a series of firms that for all other intents and purposes, run like non-governmental businesses. Since then, service has improved and the system's chronic financial problems have disappeared. That part of the free market magic works really well.

Again, it's not a totally private sector success story. The government had to set those private companies up in the first place, and they have an inside track to low interest rate loans and other occasional help from elected officials. Meanwhile, rural Japan's dwindling population has made it much harder for these companies to provide profitable service in some areas.

But this is about as free market as anyone can realistically hope for. The difference in quality and safety to what we see here in the U.S. is stark.

Their train system isn't run by political cronies. Its employees don't have the near-100 percent job security that hinders quality in government work. An apolitical profit motive spurs innovation and a drive for constant improvement.

All of the above is what really causes our transit and commuting pain in America, and Japan has eliminated most of those problems for more than a generation.

Again, we're not talking about a theoretical idea, or even some small scale pilot project. The Tokyo metropolitan is the world's largest, and this plan has been running successfully for 30 years. Promoting the idea that the Japanese model could improve transit in America sure seems like a more realistic possibility than some kind of underground vacuum tunnel.

Right now, there probably aren't enough American politicians or policymakers who even know about Japan's success story to promote copying at least some of its best qualities over here. Yet when one of the world's largest cities is getting something this important so right, it's way past time that U.S. officials take heed.

Commentary by Jake Novak, CNBC.com senior columnist. Follow him on Twitter @jakejakeny.

For more insight from CNBC contributors, follow @CNBCopinion on Twitter.