I'll admit to paying a few bucks for trades at vanguard. I don't have enough in vanguard funds to qualify for free trades on ishares etfs. It wasn't worth the hassle to me to setup another account elsewhere.
Regarding the app, the last thing I want to be doing is making trades on my phone or iPad where I think I'm much more likely to make an error, be distracted and it's harder to access other information.
From the article
The company's business model is to make money on margin trading, interest on cash deposits and payment for order flow, a fancy way of saying making money by trading faster or slower than others.
(emphasis mine). Maybe they should have said "a fancy way of saying kickback".