Apple wants in-app purchases. Why deliver full flexed apps in the web were people pays using PayPal or VISA if you can force people to use your store?
This is the reason Apple killed Flash and is the reason why they may kill any other web technology.
They later reversed that decision, of course. But the Flash decision was right at the beginning and had nothing to do with in-app purchases.
Note that Android never got Flash to work well on phones either. It just killed performance and battery life.