Ultimately you do want that doubt to go away I'd imagine, so think to yourself, what are the steps that need to be taken for the doubt to disappear? Then ask, how likely are those steps to happen?
I can only speak from the experience of not having doubted initially but then beginning to doubt... I'm still with the same co-founder in that company as we were able to work through the specific points of difference, however I can say the result is a compromised experience compared to the original vision (at least on my behalf).
Nevertheless, it is one that has had positive benefits away from the specific company in question, inasmuch as encouraging me to adopt a broader perspective on where I'm looking to find fulfillment (of various kinds), which has in turn ultimately led me to start a second company which I'm more passionate about, has a more favourable business model, and is the one I want to spend most of my time towards.
i.e. depending on your nature, there are positive externalities that can come from sticking it out, and it may actually work out holistically for the better.
That being said, it's a matter of probability; in all reality, the arrangement won't be ideal and the only value you'll extract from the process is that generic/ubiquitous 'wisdom of failure'.