FWIW, at NWP last year, we had the USAFA Prep School come visit and the number one question the free agents had was why we didn't get prep slots.
As it turns out, for USAFA anyway, admissions divides candidates into three groups for consideration: direct appointments, Falcon scholarships, and prep school. USAFA looks at the WCS scores of candidates and has different ranges for each group, in the order of DA, Falcon, and the Prep.
Many students were told that they scored too high to be considered for a prep school slot, but were beat out in their districts and/or the national waiting list. There's a fine grey line of overlap that some candidates fall into. They advised us that admissions felt we did not need what the prep school was offering. Instead, it would be more beneficial for us to take "some more advanced college classes rather than to be stuck in a remedial algebra class at USAFA Prep" (their words) and that we would be much better prepared as a result.
You also need to remember that a large majority of USAFA Prep School is reserved for priors that need some extra brushing up in academics. I believe they said around the same number of candidates get Falcons and Prep slots: 60-70 for each. This is for USAFA Prep, no idea how the other prep schools operate.