Asking questions of the CEO is different than putting questions to a regular boss. CEOs are generally more focused on the business side of things and have unique answers to questions. A few examples of good questions to ask a CEO are, "How much profit have you made in the last six months?" and "How do you think the company will grow in the next few years?"
Employees can also ask questions of the CEO that they would also ask a normal boss. For example, youcould ask a CEO where he thought he could grow as a leader. Although this may sound like doubting the CEO's efforts, it can serve to inspire lower-level workers. If the CEO can acknowledge that he has faults, then it can serve as inspiration for the workforce.
Some other questions to ask the CEO are, "Where have you failed in the past, and what did you learn from that experience?" One could also ask, "What is the priority for your company?" to gain insight into what the CEO values.
If there is something specific that an employee would like to know about the company or the company's goals, the CEO is probably the best person to ask.