This one is frustrating. I probably did 50 of what I thought were "air assassinations from trees" without getting the trophy. There are several things that seem to not count though.
One, stumps and dead/fallen trees (ramps) don't seem to count.
Two, it only seems to count if you are NOT in open combat, or combat is Yellow (not red), indicating they've lost track of you. Doing an air assassination while in red combat mode seems to not count.
Three, I've read that you have to be on a tree branch -- not perched in the "V" between two limbs -- for it to count. I don't know if this is or isn't true.
It seems to not count if you do a double-assassination. Try to target a lone guard that isn't near another one, when possible.
Progress doesn't get saved if you die, quit, or restart the current checkpoint. You have to do "something" to trigger the game to save your progress (like opening a chest, maybe, or finishing a mission, or reaching a checkpoint). So if you are in trouble, run away and recover.
A fairly good place to get this is to replay Memory 3 Chapter 3. You have to run to a few waypoints, get a couple cutscenes, but ultimately you'll be tasked with taking out several guards. There is a fallen tree serving as a ramp just ahead and to the right when this checkpoint starts. Run up the tree and through the trees/branches ahead, until you are near the guards. Go to the end, and perch on a branch. With hidden blades selected, press Square to leap down on him. Then run back to the thick dead tree you can climb up (or somewhere you can climb up), get back to the same tree on a branch, and the indicator will turn from red to yellow. Do another air assassination.
If the trophy doesn't unlock, finish the mission and replay 3-3 again.