While I'm sure there was also a financial motive, the primary was still that flash did (and does) suck. It sucks batteries, it sucks at security and it sucks at scaling for mobiles.
Conversely, Apple is in a perfect position to spearhead a web micropayment API standard, and has total control over the browser and thus the way users' use it.
My post clearly was missing the word "standard", which I've now added. Running in as many browsers as possible once something is completed is important for these things.
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.