The problem is that in the US, the powers that be don't care about public transport. The United States actually has more rail lines than any other nation on Earth. The main issue is that these are all privately owned. And for private companies, it is far more profitable to transport goods than people.

In most countries, public transport is seen not only as a national good, but a necessity. In places like Japan or South Korea, public transport is something that everyone uses and therefor their tax dollars go to making it the best, cleanest and most efficient. In the US, people HATE spending money on anything that doesn't positively affect hem directly. This is why institutions made for public use are generally viewed as "worse" than those for private use.

In general, in the US if it doesn't make money, it's not worth doing. This goes for education, health care, and public transportation. The people that use these services are seen as lower class human beings. Compare the New York City subway to the rail systems in more developed countries like Japan, Germany or South Korea. Not only is the public transportation system seen as "gross" but the people that use it are seen as gross.

But the main reason is that the companies that own these rail lines make more money by transporting goods than by transporting people. And the government has no interest in building new rail lines, because their interest is in making as much money as possible, not making lives easier for their citizens.