While I work for Google, and was involved in the CPTN and Rockstar stuff (and thus can't comment on this article at all, though I wish I could), i can actually point out that this statement is not right.
First, companies that wish to contribute to LLVM are asked to non-assert patents involved in their contributions. This is covered in the dev policy, and has been for a long time. Their are non-assertions/grants on file for a number of companies now.
As for whether Apple owns any patents on LLVM core, Chris Lattner himself told me Apple held none, which is why they had not filed a non-assertion.
Apple may or may not hold patents on LLVM code that is not "in tree" (so yes, they may have non-public frontends or backends they own patents on), and I never specifically asked about the clang frontend, but I trust Chris enough to know that if there was in-project code, be it clang or core or whatever, he would have followed the dev policy and Apple would have non-asserted them.
There is simply nothing that prevents apple from using patents against LLVM users. We can only hope that none of their numerous vaguely written patents cover any technology used by LLVM or any of their frontends like Clang.