I don't believe that Ganondorf pays his minions. I believe that his minions are all philosophically aligned with him, and believe in his evil ideals. That seems like the kind of scenario Ganon would desire. The reason they always have money, in my opinion, is because they've stolen it from Hylians they've waylaid and/or killed in the past. After all, Link isn't the only one who goes through Hyrule Field. And I do believe they trade, so the ones further away from Hylian settlements may very well trade other things for rupees.