is it operating under part 91 or part 135?
The owner can fly whomever he likes on his plane under part 91. If he charges them to fly, then he needs some sort of Air Carrier certificate from the FAA (135, 121, 125).
A corporation can own planes, hire pilots as employees to fly those planes, fly anyone willing to get on, and operate Part 91; so long as they don’t charge.
Unless the rules have changed since I was an active pilot, I believe it is within the rules to have a prorate cost sharing arrangement under Part 91.