A charter flight simply means that a tour operator / cruise line / whoever has paid an airline to fly from A to B.
What your experience of that flight is will be dependent on a) the airline which the company has chartered (it may be a well known airline that normally operates mainly as a scheduled airline or it may be one of the airlines which specialise in charters), and b) what conditions the company is paying the airline to transport you in - choice of aeroplane (and configuration), meals, drinks etc.
And yes, I think you can be fairly sure that you will be required to go through security.