SF public transportation is limited in its geographic coverage and the fact that it's not 24 hours. And that sucks. But San Francisco is also a much smaller city then Madrid, New York, Chicago, and the other places listed. Add a couple more million people to SF, South SF, and East Bay, and you can bet that public transportation will improve.
Go and visit other countries in the world. Public transportation works pretty well also in smaller cities with a couple 100.000 people. Go look to Nuremberg, Germany with about 500.000 people. Go look to Jena, Germany with about 100.000 people. Cities in France or Spain or Estland or Lithuania. Look in Denmark or Sweden.
The reason in the US is simple: you love cars.
It's about the only way to get around if you are traveling from one state to another - which we frequently do. Also, ~330M people.
I take it you mean the EU - which covers less than half the area of Europe?
http://en.wikipedia.org/wiki/List_of_cities_spanning_more_th...
Yes, a road trip in the US is cool, but I would never ever do it for just getting somewhere.
There is another nice public transport system called airplanes. Works pretty well, is comfortable, and is fast. It works also pretty well in the US. I used it several times as my frequent millage card tells me.
BTW: The US aren't that big compared to Europe. Don't mix up US and Russia, which interestingly many Amercians do, as they believe that the US is the biggest country in the world. Actually, Russia is the biggest country in the world, size wise.