I believe the term comes from using a frame of reference relating to a moving engine rather than a fixed airmass.
In either frame you can approximately relate the thrust of an engine to the change of momentum (mass flow * velocity) of the air as it passes through. This ignores cowl drag etc..
In a fixed air mass frame of reference, the momentum of the air is nil on entry and is (mass flow (air+fuel) * jet velocity) on exit.
If you solve the problem relative to a moving engine, it appears that the velocity of the incoming air is the same as the aircraft's forward speed, but the jet velocity is also increased by this amount.
The nett result of subtracting the two figures is called momentum thrust and is the same whichever reference frame you use, but in a moving frame of reference there is a large negative term for the air momentum on intake called momentum drag.
This follows directly from Newton's laws, as the force accelerating the air is required to equal the thrust reaction on the engine.