Of course, any code that requires a patent license to run isn't exactly free software either. And no free software project "with a brain" should accept code that opens up users to legal liability.
If companies like Apple and Google really are rejecting GPL v3 because of patent issues, that makes me think they want to use their patents against users of the software they are purporting to be "free." Are users of the LLVM compiler going to wake up one day to a lawsuit from one of these companies alleging patent infringement? It's all fun and games until your company is the target of a multi-billion dollar lawsuit because you shipped software compiled with a patented optimization technique or something.
Of course, the sooner that happens, the better. Because then everyone pushing non-GPL licenses will remember why those patent protections are there, and switch back. Or we could just get rid of software patents and not have to worry about the whole mess.
btw, Google and Apple probably don't like GPL v3 because of the anti-Tivoization clauses in GPL v3 that would prevent those companies from locking down the hardware they sell and preventing users from replacing the OS with a different one. But that's not really a patent issue. Nor is it a very nice thing for either company to do. At least Google does make it easier to unlock the device, even if it doesn't come that way by default.