Rupee Rush is pretty rewarding if you can nail a x2 or x3 bonus, sure. But even with a timer, it takes precision to both hit the time and collect enough Rupees to make it worthwhile, and it wasn't really my favorite minigame (in fact, it's probably the one I played the least, only doing it when I needed a Maiamai or Heart Piece from it). Overall, excluding playing minigames continuously (which is usually a great way to get cash in most games that include them), I think the monetary income rate was really well executed. Heck, even Potions actually cost enough that, until you reach the unlimited money stage (Treacherous Tower eliminates any and all need for future Rupees), they can be something to calculate or budget for.
Did you complete the Spotpass Challenges?