People should never be taken advantage of. If Khan Academy has the resources to pay people better than they should.
But, if they don't than I'm 100% with you. It's better to work on something worth doing for less money, then work on something you don't feel passionately about for more.
I joined Khan Academy as an intern in summer 2012 and have been with the company ever since. We're not going to top Facebook, but I can assure you that we compensate interns competitively. Given the massive contributions that interns like Elizabeth have made, nothing else would make sense to me.