the settings are important within media encoder. most video formats do not allow alpha layers.
in media encoder export settings. Choose quicktime as your format. then custom as your preset. scroll down and set your video codec to png, scroll down a little further and set your depth to 32. your alpha layer should render now. ask google or some other known it all for a list of acceptable adobe media encoder alpha channel formats.
We recommend dynamic link or PNG sequence for transparent export. See below for dynamic link. For Final Cut your best bet is if they allow PNG sequences.