You're almost right.

Subway and other route maps are controversial because they sacrifice intermodal navigability in exchange for intramodal navigability. In other words, a subway map is great for telling you how to get from the Red Line's northern terminus to the Blue Line's hub at Long Beach Airport. It sucks ass at telling you how to get from Burbank and Tujunga to LGB.

People rarely need to get from subway point to subway point. They need to get from, say, "Macy's" to "John's housewarming." According to the subway map, John's new house is a quarter inch from the A street station and a half inch from the E street station. Except you happen to know that John moved to E street and that if you got off on A street you'd have to walk three miles - since the space between A and E streets is uninteresting to Metro (they have no stops) they condense it down to nothing.

One of the best things I did when I moved to LA was buy two Thomas Guides, a crapton of foamcore and two cans of spray glue. I then carved up those Thomas Guides so that I had a map of Greater LA covering one entire wall of my living room. It was marvelous. It was probably 11 feet by 7 feet. I put pins wherever my friends lived. I put pins in restaurants I went to, stores I frequented. And I got me some embroidery thread and I laid out the Metro lines. It allowed me to make sense of Metro in a context of the city - because the Metro map gives you a sense that all of LA is covered:

...when in fact there are vast, unreachable swaths:

So when you see just the Metro map, you're making false assumptions. If you know where you're going and you look at a Metro map, you know it's wrong. But if you look at a Metro map and aren't quite sure of your surroundings, that map is betraying you.

Interestingly enough, it was a stone cold bitch finding the Metro stations on my Thomas Guide. People looking at street maps are rarely interested in subway terminals. Very few mapping systems take into account all the things we will use them for and consequently distort the "useless" (to them) data in favor of their focus.