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U.S. FAA FAR 91.3 ("Responsibility and authority of the pilot in command") says that:

The pilot in command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft.

When an aircraft is operating as Air Force One, it would normally be flown by the designated high ranking USAF Officer, as a military flight.

Is the President, as Commander in Chief of the armed forces, able to over-ride the authority of the pilot?

For example, if one of the current Boeing VC-25's engines flames out and the captain announces that he has made the decision to take an option/ turn back - can the President override this decision and force him/her to continue the flight?

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The pilot in command has final authority over Air Force One

Air Force Instruction 11-202, Volume 3 says the following in Chapter 1, part 1.1.1 (as in, the very first thing in the document):

1.1.1. Pilot in Command Authority. The Pilot in Command (PIC), regardless of rank, is responsible for, and is the final authority for the operation of the aircraft.

Just for fun, let's compare it to the civilian version that you referenced, 14 CFR 91.3:

The pilot in command of an aircraft is directly responsible for, and is the final authority as to, the operation of that aircraft.

Wow! Basically identical except that the military version goes out of its way to mention that rank is irrelevant.

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    $\begingroup$ And if the POTUS is with any military personnel, there is granted to be someone on board that outranks the pilot. $\endgroup$
    – Mindwin Remember Monica
    May 21, 2017 at 1:21
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    $\begingroup$ And whose authority is sufficient to make an active pilot in command a pilot out of command? $\endgroup$
    – rackandboneman
    May 21, 2017 at 2:17
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    $\begingroup$ Rank is not absolute, the military has a concept of a situational or occupational rank. For example, guards have full authority to stop higher-ranked personnel, and turn them away if they do not show the necessary credentials to enter. $\endgroup$
    – Simon Richter
    May 21, 2017 at 4:21
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    $\begingroup$ @rackandboneman - Your comment made me wonder enough that I made it a question $\endgroup$
    – Steve V.
    May 21, 2017 at 19:45
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    $\begingroup$ @E.P. -- my understanding is yes -- the 11-202 is true for all USAF aircraft. See here for an example of that instruction in action. $\endgroup$
    – UnrecognizedFallingObject
    May 22, 2017 at 1:29

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