It does, except that Samsung stated that their licensing to Qualcomm was not transferable. Also, it doesn't make perfect sense in scenarios where you have chips that implement multiple standards.
Are you really going to pay a licensing fee for radio protocols you're not going to be using ? No, if it's disabled on the chip, your device doesn't infringe and you don't need a license. So instead of paying a flat "license everything in the chip", Qualcomm sells chips without patent licenses and you get only those you need for the hardware you'll be using.
So its just a matter of facts. The courts will read the agreements and will decide what is transferable or not. The principle of patent exhaustion is sound, as it should.
Apple probably believes that it has paid for the license when it bought the chip. Samsung probably believes that the license didn't transfer. What is the big judgement against Apple here? What is so "evil" about making an argument based on the law? They are either right or wrong, but they have a right to make their case to a court of law.
It is absurd to blame a company, or anyone, for simply defending what it sees are its rights. The courts exist exactly to sort this thing out.