The most common explanation to this phenomenon which I have read is that the pressure disturbance signal cannot propagate upstream, as the medium in which it travels itself flows downstream, so signals can no longer reach the upstream part, hence flow is choked.
How I look at is, that there are a lot of particles connected to each other through springs or restoring forces, as one particle is pulled away, it exerts a pulling effect on the other particles and fluid flows. What I think is that, there is some significant time of interaction between two connected particles, during this time impulse is transferred from one particle to another. If flow velocity is too high(greater than velocity at which disturbances propagate), then the particles stop exerting pulling forces too early and the time of interaction is reduced. This lowers the impulse transmitted and the particle can no longer pull the upstream particles with it, as the time of interaction is less than adequate.
Does this make sense?