Early on I made money from brewing and selling sake, to start you can just use any nearby water but later you'll want to start using better water for better sake. Water from Misty Lake at the Scarlet Devil Mansion for regular sake, from the bath house in the Underworld for strong sake, and from the lake on the Youkai Mountain Summit for sacred sake. I don't really know the other sake recipes though, since they were added after I no longer needed money so I haven't done much more brewing.
Beyond that I made most of my money from gambling in the Scarlet Casino. With some starting charisma and a capped speech skill, the dice game can make tons of charisma. You'll need to gamble a bit then leave and re-enter to unlock selling it at the casino.