The theory is that each company has enough patents that it acts as a sort-of nuclear standoff, but in Apple and Qualcomm's case the "mutually assured destruction" scenario hasn't proved sufficient
The problem with the "mutually assured destruction" theory is that for the standoff to be successful, each side must be able to inflict devastating damage on the other side without gaining much from it. However, even though we often joke that only the lawyers gain from these fights, most of the money that a company stands to lose is directly given to the other company, so it's (mostly) a zero-sum game.
If each company think they can with $1 billion from the other in patent payments, then it's worth it to spend a few millions to the lawyers just in case you win your lawsuit and the other side loses theirs. The mutually assured destruction principle would work if, say, 90% of payments were swallowed in taxes and/or legal costs. Then each side would risk losing $1 billion in order to win at most $100 millions, and it would be an efficient deterrent.