This is why I prefer my subway commute to any of my driving commutes; spending a half hour driving is a half hour wasted, but I can read on the subway. I liked my walking commute best of all, but I can't always live within two miles of work. I don't have a problem with cell phones (Note to NYC: Never let anyone wire your subways for cell phones), only morons who need to play their music so loud that even using headphones, it is clearly audible to people at the other end of the car.
Of course, in both cases the problem can be partially solved with earplugs. And for Amtrak, as well as a few other train lines, there is usually a quiet car where cell phone use is prohibited. Man I love those cars.