The issue is that we're talking about standard-essential patents, not just patents. And it was, in part, Qualcomm's choice that such patents be standard-essential patents.
If you want your patents to be essential to certain industry standards (e.g., how cellular communication works), then you have to agree to license those patents on fair, reasonable, and non-discriminatory terms. If you don't want to do so, then you don't get to have your patents be essential to such standards. You don't get to have your patents be incorporated into standards, such that everyone in an industry has to - for all intents and purposes - use them and thereby have demand for the licensing of those patents created (or thereby gain other benefits which you perceive), and then refuse to comply with the conditions you agreed to in order to get those patents to be essential to those standards.
Qualcomm could refuse to agree to FRAND licensing terms if it wanted, and then have more onerous licensing terms for certain patents. But then others would be less likely to license those patents, at a minimum they wouldn't have to license them in order to, e.g., build and sell phones that work with modern cellular networks.
If the accusations in the complaint are true - e.g., that Qualcomm made phone manufacturers pay higher royalties if they bought baseband processors from Qualcomm's competitors rather than from Qualcomm or that Qualcomm refused to license SEP to its competitors - then it should be prevented from doing those things. Further, if those accusations are true, it will almost certainly lose this case or be forced to settle - and agree not to do such things.
Again, there is a major difference between having a patent and having a standard-essential patent. If you want the benefits of the latter, you have to accept the responsibilities and commitments that come along with it. Otherwise, having industry standards - regarding, e.g., how Bluetooth or USB or WiFi function - won't work.
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https://www.ftc.gov/system/files/documents/cases/170117qualcomm_redacted_complaint.pdf