Our characters aren't out buying Ferraris or $3,333.33 ice cream sundaes; they're buying cities and people. Money doesn't just buy you cool stuff in The Jew of Malta: it buys you power. And in this play, power is the coolest thing of all. Ferneze has to pay off the Turks to keep Malta safe; Barabas gets the friars off his back by offering them money; the Spanish offer to help Malta largely so that they can sell slaves on the island. It's definitely a rich man's world. In a universe where having the upper hand is way more important than being moral, money ends up being the main indicator of advantage.
More than religion or revenge, money is the main motivational force in this play.
While money starts out as the main issue (Ferneze's need of it, Barabas's lack of it, the Turks' demand for it) by the end of the play other issues (questions of religious, political, and national identity) have taken center stage.