The reason Sonny hesitated was that the sight of that empty chair drove home the reality that his father had been shot, could still die, and would not be occupying that spot for a long time, if ever.

It would've had the same impact of noticing the favorite chair or seat at the dinner table of a family member who had just died or become gravely ill. A very sobering moment. No one would want to be the first to occupy such a spot so soon after the initial tragedy.

I'm not convinced Sonny 'doubted' his own abilities in the role suddenly thrust upon him...but it surely would've dawned on him that he was about to step into a BIG pair of shoes.

Yes, Michael would later sit in the chair effortlessly and with no thought whatsoever, and YES...this may have been FFC's not so subtle symbolism at Michael's eventual rise...but he had also been away from home, apparently estranged from the Don, and up to this time not impressed nor interested in the Family Business run so successfully by 'pop'. While concerned for his father of course, the chair itself may have had little emotional impact on this family 'rebel'.

Apple