Be pragmatic: there will be other opportunities which are equally interesting and staying isn't helping. You could be CTO at a different startup. Further, you should be approximately at your zenith at the company and they should be able to provide a strong reference, if you stay dissatisfied your performance and appearance will suffer - along with your potential for future employment.
Also happiness is about the journey (career, parenting, etc). If you're not on a journey you won't be happy!