Netflix is going to exist regardless of whether Amazon lets them run on AWS.
Amazon letting them run on AWS is brilliant as they get a piece of Netflix's pie. So even if Netflix beats Amazon Prime, Amazon gets to dip into their pot via revenues from AWS. It's a great hedging of bets.
They're totally separate businesses. The people that treat Netflix like their customer aren't the same people making strategic decisions about Amazon Prime. Amazon is a ridiculously large company.