The reasoning given by my driving instructor was that this secures the vehicle and makes things just a little more safe for everyone.
If I am stopped in traffic with my parking brake on and sometime lightly rear-ends me, my vehicle may not move at all. If my parking brake were not applied, the probability of my vehicle not moving at all drops significantly.
If I am rear-ended without the parking brake applied such that my vehicle rear-ends someone in-front of me, I am partially responsible for the damage caused ahead due to my failure to secure my vehicle.
This is only tangentially related to taking my foot of the clutch. I depress the clutch in order to apply the parking brake correctly. Once the parking brake is applied, I simply have no need to continue to depress the clutch.
It takes me very little time to apply the parking brake and then release it and so I tend to do so when stopping for more than a second or two.