I don't understand the confusion here.

It's not just Cape Air, ALL part 135 operations carrying passengers under IFR must have an SIC unless they are authorized to use an autopilot in lieu of them.

If you were flying charter pax IFR in a 172 w/o an autopilot you would need an SIC.

135.101

"Except as provided in Sec. 135.105, no person may operate an aircraft carrying passengers under IFR unless there is a second in command in the aircraft."

135.105

"(a) . . .a person may operate an aircraft without a second in command, if it is equipped with an operative approved autopilot system and the use of that system is authorized by appropriate operations specifications.

(b) The certificate holder may apply for an amendment of its operations specifications to authorize the use of an autopilot system in place of a second in command."

It's that simple