Plus the costs of running the cafe! Plenty of HNers know how crazy Bay Area rent is. Business rent is just as much of a rip. It's $6 for a 12oz mocha because they have to pay a ton for space, taxes, labor, supplies, equipment, power, water, etc.
Actually I would say $6 for a 12oz mocha is (presently) still a rip-off. It might not just be you that's getting ripped off though, I talked to some guys who opened up a Boba joint and they were getting taken for a ride on their lease for a space they were subleasing from another restaurant, which was the main reason they went out of business. From the amount they quoted, they were probably paying the entire restaurant's lease, which is to say, some small business owners are unable to successfully negotiate a good lease.