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Couple of reasons:
1. cheaper
2. can streetrun without issues
3. sharper cornering and higher grades
When used properly it works really well. LA is a good example, all metro trains have total right-of-way at all times so they do not stop like a real train does but can also handle tight maneuvers a 80' cars wouldn't. Trains can be made long enough to deal with demand in city cores, but short enough where they aren't running empty as it gets further away from the core. Core stations have appropriately high frequency while suburban stops are more modest.
Now where LA is great at it, SF is shit. Muni is never faster than car traffic because Muni trains do not have right-of-way, and the trains themselves are never put into lengths that are appropriate to the demand. Crowded platforms are common because 2-3 trains are needed to do the work, but the scheduling is never done right because it's done by bus planners and not people experienced with rail operations. This is especially galling when comparing Muni to the BART trains above them in the Market St subway. Because of this trains are always stopping everywhere and clogging up both ends of the tunnel, so there is never a clear shot.
Likewise the Bay Area does commuter and regional rail very well, owing to the success as a safer alternative to BART and one that services areas outside the traditional Bay Area core. LA gets commuter rail wrong because Metrolink is shoved between freight trains in one of America's heaviest freight corridors, and Metrolink preforms a lot of intra-LA service that is better handled by LA Metro while their regional trains compete unfavorably against the Surfliner (which also has more political support in Sacramento).
Point is, the quality of the overall system is fitted to what people demand and what politicians can order. The actual composition and structure of the system reflects how people live.
