What factors affect the propagation delay at wireless communication? Generally, the signal propagation delay is d/c.
d is a distance between a transmitting antenna and a receiving antenna.
c is light speed.

However in NS-3, there is Random Propagation Delay Model

Random Propagation Delay Model: The propagation delay is completely random, and changes every time the model is called. All packages, even those that are sent between two fixed nodes, experience a random delay. As a consequence, the order of the transmitted packets is not maintained.

What kind of communication environment does this model take into account?

I think the obstacle, etc is considered. But because I can't find any official document or paper, I'm not sure about this.
Even if transmitter and receiver are fixed, you have unknown reflecting objects, resulting in unknown multi-path propagation. The resulting propagation delay can be modeled as a random variable. If there are moving objects in the environment (such as people moving in a room), then the propagation is not only unknown but also time-varying. The delay spread of a channel describes the difference between the maximum and the minimum propagation delay in the given environment.