For thunderhawk flights, it was stated i the flying transport rules that it transport units. Can we transport heroes as they are not officially unit, but count as unit when moving?

That is a good question. Though I thought that you could and replied as such to the same question asked on another thread, after doing a thorough read of the rules I am of the mind that they cannot. I guess we'll have to wait for an offical answer from FFG.

A: Heroes are units for all Movement Orders effects.  The rulebook explicitly states that they are also units for routing, retreating and event cards.

B: Flying Transport is a special ability. 

The question then is whether or not the Flying Transport special ability is considered part of the Movement Order's effect.  If it is not, heroes couldn't be picked up as they are not considered units.  If it is, Heroes can be picked up, and they take up one 'slot' of transport capacity.

I realize I didn't answer the question.  I figured this was just a good way to sum up the problem.

Thematically (and logically) the later option sounds like it makes sense, as I'd say the special ability is still part of the order card's effect, as it's triggered by the card.

And , it would seem very odd, that a Hero couldn't follow it's supporting units.