Steven W. answered 07/30/19
Physics Ph.D., college instructor (calc- and algebra-based)
I think the problem is you are crossing up the RESULT of no net force with the presence of the forces themselves. Newton's 2nd law states that net force = mass * acceleration, relating the net force to the resulting acceleration of the system.
If we look at a small section of the rope at its center, it will be pulled into two directions by tension leading away one way along the rope and tension leading away in the other. As you state, these two forces will cancel out. This results in zero NET FORCE, and zero acceleration, as per Newton's 2nd law. However, the lack of a net force does not mean the individual forces are not present.
It is similar to imaging how you may be sitting or standing now. If you are stationary, the net force on you is zero, and that may be due to the force of gravity and another force (perhaps a normal force) on you cancelling out. However, the fact that these forces cancel out does NOT mean the force of gravity on you is zero.
Also, not all forces act at the center of mass of an object or system. That is only generally applied to forces exerted by a field, like gravity.
If you have any other questions, please do not hesitate to ask!