They have survived the internet revolution where other businesses have been disrupted. No startup is even close to chipping away their collective control. So they are empowered to do as they please.
One way a disruptor could tackle this is by providing all (or even almost all) of those fees as cash back - giving everyone 2.5% cash back regardless of their creditworthiness / ability to get a sweet rewards card would be very popular. But then you'd probably want to not do that at merchants that aren't accepting traditional credit cards, and I'm not sure how customers would feel about this.