Subway maps are a distinctive subspecies of maps that sacrifice geographical accuracy for clarity. Here is a normal map of Washington DC:
And here is the Metro Map for the same area; note what happens to the river.
The Metro map is much more graphic, with all its bright colors and neat lines, but it only loosely reflects reality - just enough to be useful without being confusing. The challenge for the designers is to find the right balance between simplicity (so that riders can easily figure out routes) and context (so that they can figure out how to get somewhere once they get off the subway). An endemic problem with these maps is that it skews the apparent distance between stops, disguising trips that would be faster on foot.
The London Tube map was the first map to use stright lines instead of actual routes; it is generally considered a classic design, but one that doesn't always transfer well to other uses; some uses of the style are spectacularly unsuccessful. (For an interesting route map of the world, go nearly to the bottom of this page, to the Aug. 29, 2006 entry.)