Why so noisy?

Grid Chicago asks: why doesn't the Metra run as smoothly as the German Regio/S-Bahn system?

This question puzzled me for a while as well, and I remember during my first trip to Germany as a freshman in college, I was astounded at how quiet and timely the trains in Munich were. In the US, we're rather used to trains making a cacophonous racket as they enter and leave the station, screeching and clunking and grinding, but the trains in Germany seem to glide in on air exactly on schedule, only the whine of the A/C motors and whoosh of the doors opening and closing making any peep at all.

So why are U.S. train systems so loud—are the laws of physics not the same? How does Germany run on time? It turns out, there's a whole bunch of reasons:

• Yes, money is important. Track noise isn't really about straightness, per se, but Germany spends a lot more on things like welded rail (no clunking over joints between individual sections), track ballast (which deadens the noise and vibration), wheel truing (which prevents the clack-clack of flat wheels formed when the wheels lock or slip during braking), and signal systems (which are often the source of delays). The trains are also a lot newer (more responsive suspension systems) and run on electricity (smoother acceleration, no fumes, more reliable). 
• Why do they spend more money? Well, more people use the train—people in the US are reluctant to give up their cars, largely because of last-mile problems, particularly in the suburbs. Whereas a lot of small towns in Germany have light rail systems within their compact urban cores, US suburbs are sprawling and usually have limited to no transit, meaning you'll need a car to get to your destination one way or another. Limited ridership base = less frequent scheduling, although that sadly perpetuates a cycle of low ridership, because people don't take quick trips on lines with poor frequency.
• Track/grade separation of passenger and freight rail. The US lags way behind Europe and Asia for passenger rail, but what many people don't realize is that we're actually way ahead for freight. But that means freight reins supreme—many rail passenger routes in the US are leased from freight companies that own the rights of way. Freight is a whole different game logistically, though, and it severely affects the reliability and scheduling frequency/flexibility of passenger trains. 
• Network layout. US systems are generally designed as hub-and-spoke, oriented around urban cores, whereas Germany has a web-like blanket of rail service that means you can often find a more direct route between places. This goes towards ridership, investment, etc. The US had more routes in the past but they've mostly been pared down to urban commuting corridors.  
• Federal Rail Administration regulations. Trains in the US are extremely heavy because of stringent crashworthiness laws. Heavy trains have more sway, take longer to accelerate, can't corner as tightly (see: Acela's tilting train fiasco), and make more noise. It also means it's much harder to procure modern trainsets, because the world's train manufacturers don't have standard designs that meet US regulations.