In a nutshell, I think the basis of the problem is that PTs are trained to apply a version of the medical model to rehab: what structure is damaged? and how do we fix that structure? In most cases, this analysis is flawed, and it is almost always flawed when applied to athletes, because it fails to consider the System of which the structure is a component.
I've bitched enough about this. But we have two guys here, Will Morris and John Petrizzo, both SSCs and both PTs, who can address the issue productively. In fact, John has written an article about this, which will run very soon.