My options to getting to SF: Fly to OAK: $2002 (main cabin) with a travel time of 12:17h, and two layovers (driving is only 11:43h). Fly to SFO: $411 (main cabin) and a 2:09h direct flight. I really don't understand airline pricing.

Price difference makes sense given the routes. It costs the airlines more (in both fuel and opportunity) if you take three flights instead of one short flight.

Better questions: • Why doesn’t this airline operate direct flights to OAK? • Why offer such a convoluted route at all when they could just tell you to fly to SFO instead (and then take BART if needed)?