Not any, many were rebuilt after bombings in WW2. Even so, Germany is known for splendid trains, meanwhile Bostons trains are notoriously bad. My old company was off the red line and numerous employees were delayed at least once a week due to the red line sucking.

You'll find people who regularly use public transit in many European cities complaining about their transit systems too. Boston isn't great, especially in the winter. (I used to have to use it on a regular basis.) But if I'm being fair Boston isn't "notoriously bad" unless you're setting the bar at the level of a relative handful of world cities.

While many European cities were substantially rebuilt after WW2, the existing layout was usually retained.

Boston and metro Boston also have a pretty high population density, so it doesn't help that early roads were laid out by cud chewing surveyors.