These are most useful at getting around a map to build lodestones as well as for making watch towers and strongholds to keep enemy forces back, and build trebuchets within range of your enemy. They can build in elevated places no other unit can get to.
They are also good for clearing out paths for your units to get through, removing vegetation, debris from destroyed buildings and ships, and the remains of units turned to stone or ice.
The ability to easily get near your enemy, and build factories to produce units closer to them, thus less travel time, can be useful in some situations.
You can also fly over and build walls everywhere, irritating your enemy to no end. This is a rather lame tactic, since it confuses the AI, and against a human opponent just makes things more tedious.
Sometimes, the only way a Aramon player can expand in some areas is via a Flying Builder. Since Flying Builders can fly, they can reach places other Aramon units can't and establish bases there.