The two people I spoke to gave several reasons:
* PCT thru-hikers seldom use Whitney Portal for resupply. Most go from Walker Pass to Kearsarge. It is easier to walk out via Horseshoe Meadows, too.
* Many PCT hikers were paying for the permit thinking they needed it to summit Mt Whitney.
* PCTA felt their hikers shouldn't add to the crowding already on the Whitney Main Trail.
They did not mention any troubling incidents or anything like that.