Why do adherents to the priesthood of all believers still have organized congregations? I might be making some naive assumptions here, but I have a hard time seeing what the purpose of congregations are in the context of priesthood of all believers.

As I understand it, priesthood of all believers basically says that all people have direct and equal access to God, as well as equal privilege and authority to minister. What then is the purpose of congregating? Why are those congregations well organized?
The purpose of congregational gathering is not exclusively to provide the laity access to someone who can be a mediator between them and God, so the assumption that the priesthood of all believers is mutually exclusive is invalid.

Gathering as a congregation has many purposes, including mutual edification, encouragement toward love and good deeds, instruction in the word, serving one another, community, etc.

So, the biblical idea that we all have one Mediator between us and God in no way precludes the call to fellowship with one another.