Hmm, how big is this company? I can't imagine a startup with a CTO that doesn't actually doing any coding until well beyond the bootstrap stage, this seems odd to me.
Unless your are failing to get your code working there is almost no good reason to tell you to leave, this seems like some sort of power play. I would tread carefully if I were you. Even if they did decide it's better off without you "Expect to leave in 3-6 months" is a giant WTF? Why tell you now unless they are going to sweat you to give up equity. Telling you you aren't a good coder is a good way to get you to feel like your contribution to the company is less than it really is, but it sounds to me like you must have done all the work. Even if this CTO helped with the scope and guidance to get everything going better, what would they have if you took all your work and left with it? (Not saying you should try that, just realize how much of what is important did YOU actually create) Unless almost everything you've done is getting thrown out, you are probably undervaluing your contributions, from what you've said.
Unless your are failing to get your code working there is almost no good reason to tell you to leave, this seems like some sort of power play. I would tread carefully if I were you. Even if they did decide it's better off without you "Expect to leave in 3-6 months" is a giant WTF? Why tell you now unless they are going to sweat you to give up equity. Telling you you aren't a good coder is a good way to get you to feel like your contribution to the company is less than it really is, but it sounds to me like you must have done all the work. Even if this CTO helped with the scope and guidance to get everything going better, what would they have if you took all your work and left with it? (Not saying you should try that, just realize how much of what is important did YOU actually create) Unless almost everything you've done is getting thrown out, you are probably undervaluing your contributions, from what you've said.
Good luck.