Qualcomm double dipping (charging chip vendors & their customers) is plain unfair. The only thing they aren't doing is sending IP notices to end users of phones, like you & I.
That said, sympathizing with Apple is hard. Ironic for a company that hardly allows any freedom on it's hardware (blocking NFC for 3rd parties for instance, requiring MFI certification for accessories at a steep cost) or app store (ultra strict, often whimsical app approval policies that stifle innovation) to cry foul.
Apple & Qualcomm deserve each other.