Why “Flytower”?
Flytower started at a student theatre. It was built to run the Minecraft server for the Nottingham New Theatre, so when it needed a name, it took one from the building rather than from the game.
What a fly tower is
Look at a theatre from the outside and you will often see a tall, plain block rising above the stage. That is the fly tower. Inside it, scenery hangs on long metal bars called battens, high above the audience's sightline. When a scene changes, a crew member pulls a line and a whole set flies in on cue, ready to play. When it is done, it flies back out of sight. A busy show can have dozens of pieces waiting up there at once.
Why it fits
That is what Flytower does for Minecraft servers. Several servers hang in one box, each on its own batten: its own user, folder, memory and address. You bring one in, take one out, or swap in a new world, all from the panel, without anyone climbing up into the rigging with SSH.
The logo is that picture: three battens under the grid, with the lowest one lit in amber because it is the one “in” right now.
Why not something blocky
Minecraft already has a look, and it belongs to Mojang. Rather than imitate it with grass, dirt and pixels, Flytower borrows the backstage palette: amber like a tungsten work lamp, cool steel like the rigging, a green “go” for a running server and a blue backstage light for notices. It also means Flytower never has to pretend to be an official Minecraft product, because it isn't one.