On another note; how much liability does the pilot take on? If you work for the FBO (I don't) as a pilot and it turns out that someone at the FSDO decides that flight was an illegal charter do they go after the poor helpless pilot that had no idea who owned the airplane or what arrangements were made by the FBO?
The issue of holding out isn't really relevant, but the issue of operational control certainly is.
As a pilot, you always share in operational control. How much liability does a pilot take on? If you're the PIC, all of it, all the time. That's why you're PIC...you assume ultimate authority for the flight, for the safe outcome of the flight, for the legality of the flight, for the airworthiness of the aircraft, for the actions of the aircraft, and the resulting fallout of all of it.
If you flew cargo and didn't ask what was aboard, and upon landing learned that you'd just hauled a hundred kilos of cocaine, do you think you might be held responsible, even though you didn't know what was aboard? Of course you would. You are responsible for knowing what's on board.
Is a pilot who doesn't know he's flying an illegal charter (yes, there is absolutely such a thing, and yes, there is absolutely an illegal weapon) responsible merely because he failed in his duty to determine the legality of the flight before agreeing to undertake it? Absolutely, yes. You're required by regulation to become familiar with all aspects of the flight before you accept it or undertake the operation. Remember 14 CFR 91.103? It doesn't just apply to runway lengths and fuel. It applies to EVERYTHING.
The FBO providing the aircraft and pilot, and accepting money or compensation to transport persons or property from one point to another. This is the essence of a 135 operation, being performed without a 135 certificate...lacking the certificate, this becomes an illegal operation.
The fact that another company owns the aircraft (other than the FBO) is largely irrelevant, except that the other company that owns the aircraft shares in the liability. The ownership doesn't affect the legality of the charter operation. The FBO has obtained by lease or agreement an aircraft, and is providing flight services to a client. Those flight services include provision of aircraft and pilot; the services are transportation by air for compensation or hire from one point to another. The FBO enjoys operational control.
A company for whom I flew some years ago was affiliated with another company that did something similiar to this. The affiliate company (I'll call Company B) was approached by the CEO of a major insurance company with a request for corporate services. Company B leased an Astra and a Lear, and performed in the capacity of a corporate aircraft for the insurance company. Company B held a 135 certificate for small piston airplanes, but did not attempt to include the turbojets on the 135 certificate. Company B asserted that the turbojet operation was for one client who had full operational control, called the shots, made the arrangements, and flew only their own personnel on company missions, and didn't accept compensation from any passenger.
Company B provided the aircraft to the insurance company, for a fee. Company B's position was that they were leasing the aircraft to the insurance company. Company B also provided the pilots, and later attempted to have the insurance company pay the pilots to get around any issues there.
The FAA proposed very large fines, revocation of the pilot certificates, revocation of Company B's 135 certificate, and shut the operation down.
The soloution for company B was to get rid of the Astra, and take a Lear from the company for whom I flew. From then on all flights were conducted under 135, on our company certificate, using pilots on our certificate, and the FAA was happy.
I don't have time to research them right now, but numerous legal precedents are available regarding this issue...especially companies trying to form loopholes or dodge the regulation by setting up their own avenues to avoid Part 135 certification and cost.
Regardless, the pilot most certainly can be violated for taking the flight. Ignorance is no excuse, and is a poor reflection on the pilot. It's the pilots JOB to know what's going on, and most absolutely will the pilot be held accountable for that knowledge. Ignorance in a pilot is never a positive attribute.