Are transit fares in Los Angeles cheaper than in San Francisco? That's the impression you'll get from a direct comparison of the base adult cash fare. The travel blog Price of Travel just compared the base fares of 80 major tourist cities around the world, and noted that while San Francisco Muni's base fare is $2.00, that of the Los Angeles County MTA is $1.50.
Yes, but San Francisco offers a free transfer, so that a $2.00 fare takes you anywhere in the city. In Los Angeles, you can travel along one line for $1.50, but many trips require a connection, and in that case you'll pay $3.00.
The journalistic temptation to cite and compare base fares is one reason that transit agencies feel pressed to keep that number low, which in turn pressures them to raise revenue other ways, such as by charging for transfers. It's a bit the way budget airlines work, offering huge discounts but then charging fees for all kinds of things.
Los Angeles County transit agencies also labor under a peculiar funding arrangement in which a certain countywide funding source is allocated according to fare revenue divided by base fare. So if you keep your base fare down (by charging for "extras," such as connections) you get more money from the county! This formula was intended to be a proxy for ridership, which is hard to measure, so one hopes that once smartcards become a reliable way to count riders, the formula and its perverse consequences can be left behind. Of course, the real challenge will be to count complete passenger trips rather than boardings. (The latter are easier to count, but double-count trips requiring a connection.)
Even Southwest Airlines will sell you a ticket from your origin to your destination, rather than making you buy each segment separately. In fact, the ticket from A to B via a connection at C usually doesn't cost more than the ticket from A to B nonstop, because the airline recognizes that you're changing at C for their convenience, not yours.