The difference is that Qualcomm agreed to FRAND (fair, reasonable, and non-discriminatory) licensing terms in exchange for their patent being included in the standard.
Once they got their patent in the standard, now they're saying they get to charge whatever they want.
That's the problem. That wasn't the deal they and everyone else agreed to, and it's too late to remove their patent from the standard.
Contrary to your unsubstantiated claims, Qualcomm's licensing rates are publicly available and published time to time -- often in the range of 3% to 5%. Apple according to this article pays nowhere close to the published rate that most other handset makers are paying.
So in mobile devices, Qualcomm's wireless patents do deservingly get per device royalty whereas, for automobiles, it would make no sense to use the same per device royalty.
On a somewhat unrelated note, Apple demanded the entire profit on per device basis for a couple of frivolous design infringement from Samsung and won a couple of years ago. This absurd, biased lower court ruling was overturned by the Supreme Court last year.