For Negan, of course, that's precisely the appeal: In Daryl he sees all the strength and conviction he's maybe lacking otherwise in his team, and he knows that he if can charm him onto his side, his empire will be all the more unstoppable. But he also knows there's a limit. Daryl's refusal to submit may be a virtue, but it's not a virtue Negan can do much with if it doesn't have a breaking point somewhere. There's no way a leader like Negan can be expected to tolerate this kind of refusal for more than a little while. He'll need to settle the question of Daryl soon, either by finding another way to persuade him or by (regretfully) killing him off.
So is Daryl not long for this Earth? Unlikely: Negan seems too invested in his potential as a comrade to pull the trigger, and Dwight, his second in command, is having the kinds of doubts about his boss’ leadership that could compel him to keep Daryl safe. (Besides which, the show just axed two beloved major characters -- killing off another fan-favorite so soon would be much too brazen.) But should Negan find the urge to extinguish this wily dissident too overwhelming to ignore, we're in for some kind of confrontation, even if it doesn't prove fatal. No matter what, things can't stay this way forever.