Most people involved in a pre-textual motor vehicle stop and issued a warning for a trivial non-offense won't know to say the magic words that begin their legal defense: "Am I free to go? Why am I being detained?" and when the polite officer says, "Well, I'm sure you've got nothing to hide, let me search your vehicle, and no matter what I'll make sure you're on your way quickly," many quickly hope compliance is their best option in the short-term.
So they say, "Yeah, go ahead," instead of the alternative, "I do not consent to search and invoke all protections afforded me by the Constitution; while I am cooperating within those constraints, please advise me promptly when I am free to go."
You'll get searched anyway, whether it's your phone or your car. You might get arrested anyway. But having invoked your rights instead of freely waiving your rights gives the defendant ample opportunity to assert their innocence in court without having already accidentally proven their guilt without the benefit of counsel.
I expect most people, despite the Supreme Court ruling, will find their phones searched anyway; consider stop-and-frisk in New York City. Please set a passcode on your device, preferably alphanumeric instead of a simple PIN, and avoid interacting with law enforcement, they have better things to do than read a neckbeard hacker's text messages to his mom about picking up more Mountain Dew at the store.
(Nevermind Border Patrol checkpoints in the US or Customs/Immigration interviews...)