We have also made our own arrangements in recent years, since the choice of operators diminished to just Olympic and also having realised that the flexibility of making one's own arrangements really does make for a better holiday, for us at least.
This year, we booked with Olympic as a last minute decision that, in retrospect, I really regret. It wasn't that much cheaper, either. Booking an apartment directly and either hiring a car at Heraklion or having the apartment owner book a reasonably priced taxi, works well and is a nice start to the holiday.
Having travelled elsewhere in Greece using the excellent and reasonably priced public transport - even on tine islands - I don't know why we haven't done this for trips to Plakias. I agree whole-heartedly with the post somewhere above where Mike makes the point that it adds to the enjoyment of the holiday. We will be back late in September, think we might try this.
Richard