It's a choice by the airline - if they handle their bookings through it, then also direct bookings will go there because they need to have a shared view such as

It's a choice by the airline - if they handle their bookings through it, then also direct bookings will go there because they need to have a shared view such as knowing what seats are available/sold. There are various tiny airlines that book directly, but the vast majority of flights aren't with them.