If you book a flight to Heraklion with Thomson, you can also book a place on their coach transfer to Ierapetra for £12 (presumably one way). The 30 min onward transfer to Makrigialos would be around €25-€30 by taxi, or if the timing is right, €2.60 by bus.

we tried this in September and is fine as long as you are happy for the trip to take anything up to 3 hours just to get to Irapetra as it drops off all of Thomson holiday makers to their hotels and apartments. Cheap transfer but not ideal when you get to Irapetra in the early hours of the morning. Luckily we had arranged to pick our hire car up there and the road to Makrgialos was quiet at that time of the morning but would not look to do this again on a night flight.