Probably their lawyers got to them. They have a near monopoly in legal music downloads (market share at 70%), so if their app store policies led to Rhapsody or Rdio going out of business it would look pretty bad in the eyes of regulators.
I think it's rather that Apple figured that those two (and others) going out of business (or at least ditching iOS) will hurt their platform more than anything they'll gain from the subscription rule change.