The word owner sounds more generic as it applies to a lot of things. While it is common to see people referring to themselves as owners of various businesses and establishments, the word can also be used to describe someone who owns something. This means so far something belongs to me, I'm equally the owner.
This is just to say the usage of the word 'owner' should not be limited to businesses alone. In other words, once you own something and you have exclusive rights over it, you are the owner. On the other hand, CEO or Chief Executive Officer is just a title for someone occupying the highest position or having the highest rank in a company.
Usually, a CEO is regarded as the owner of a company or an establishment, but, at times, the title can be used for another person other than the real owner of the company. In a situation where the CEO is not the owner of the company, people usually rise to that position based on appointment.