I hope you get a reply to your question as I am having the exact same issue on red harvest, as I posted on another ARMA forum:
"This is obviously a very simple question but I am stuck and my google searches are not helping.
I am playing red harvest and want to call a chopper to help me move around the map.
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I have summoned a transport copter and after a lot of fiddling around managed to get my squad onboard.
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We are now sat hovering 3 feet off the ground and the chooper will not go anywhere.
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Again after much searching I found out how to set waypoints and I went to the map and "shift and click" near the taget zone and then communicated on the command menu to move to the new waypoint but it seems like I am just telling my squad and the chopper does not move.
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How do i get the transport chopper to move me to where I want to go please?
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Thanks"
Someone helpfully directed me to a script you can add to get the chopper to work but surely there must be an option in the game that makes this function actually work!