This is in contrast to Philadelphia, where everything goes through Center City. There's no easy way to get from one part of the system to another if they are not on the same line. It really is "commuter rail" while the NYC system serves everybody, not just commuters.
This is partly because (or has caused it be) that there is no "downtown" in NYC, no Centrum, as they call it on the European highway systems. "Downtown" means "South" not a destination. Instead there is a collection of geographical centroids, neighborhoods, that are fully equipped with all services for businesses and residences. I am not exaggerating the fully equipped part. It's not surprising, I suppose, that I'm a block away from half a dozen dry cleaners or places that will make me a pizza. But I'm also only a few (4) blocks away from a lumberyard and a place that sells marble and granite, and one block away from the most fully stocked plumbing supply store you'll ever see.
Not to mention the place where I get my shoes resoled.
So travel is between these neighborhoods, all mixed residential and commercial, with some neighborhoods, like mine, more residential than not, while others more commercial than residential, like the financial district. This can only work, or can only have come about, if you can get anywhere from anywhere.