Mike and I have sort of started this topic under "Sun Beds" but as there is enough irrelevant material already under that topic I thought I'd start a new stream.
I like to travel independently for many reasons but, of course, my big disadvantage is the transfer.
However, I always use the local buses to get from Iraklio Airport to Plakias (and from Chania to Paleachora) and return. They are cheap, comfortable and reliable. You just have organise your timings and be prepared to wait around for the odd hour here and there.
Admittedly it makes a difference that I travel alone. A taxi costs minimum €100 each way whereas the one way bus fare this year for one person is €13.20.
I would encourage more people to use this option.