My worst was 5½ hours Heraklion to Plakias. This was many years ago, and if I remember correctly it was with Thompson. Yes, there used to be a choice of tour operator. At one time there were seven different UK companies offering holidays in Plakias.
These days, you don't always get a transfer with Olympic, but we don't use them if they are offered.
Taxis are a faster and more convenient option - or get someone from Plakias to pop out and pick you up.
Our normal solution is to hire a car at the airport. If you deduct the cost of taxis each way then it costs little extra to have transport available - to go for dinner in Sellia, or seek out a sheltered beach if it's windy in Plakias.