I just like to fish for stuff. Just make sure you get your wallet upgraded first (which you've probably already done). Most of the minor glowing spots are rupees, and you don't get to put them back because your wallet's full. (Ironic that when such a feature was introduced in TP, it was just annoying. But I digress.)
Alternatively, just sail around for a while until those barrels start appearing with the flags. Then sail between them and barrels with rupees above them will start appearing. It takes a while, but if you get good at the game, they really add up.
You can also sell stuff to Beedle, but I haven't tried it yet.
There's also the mail-sorting mini-game on Dragon Roost, but I'm not very good at it so I can't make much money that way.
Those boats that shoot bombs at you sometimes drop whole chests of rupees that you can then fish up with the Grappling Hook. Even when they don't, they (like many enemies on the open sea) often drop those color-changing balls. If you're quick with the boomerang, you can hit those when they're green and then pick up most of the rupees.
If all else fails, you could always politely suggest to Tingle that you need the charts deciphered because you're saving the world and his sorry hind end along with it. I'm sure he'll give you a discount. Tingle is always so
reasonable. Right? ...Right?