I've seen that before. At least in my context, this happened because the CEO did not see the CTO as anywhere near equal at all. Instead, the CTO was the CEO's "tech guy". And because he was considered the best or most important tech guy, the CTO got his title.

Sorry about that, but it sounds like you should consider the possibility that the CEO sees you as just another employee (with a fancy job title). In that mental state, it would mean a waste for the CEO to include you into his decisions.