doing it through compressor is not going to help as the resize options are not there like they are when you do an .mov
what I do is export from fcp as quicktime conversion and set the size to 640×360 prores codec.
take that into compressor and use a windows media preset (have flip4mac here too)
if it still looks ugly, make it closer to the size it’s supposed to be when you do the export quicktime conversion from fcp.
the windows media export has no function for ensuring the resizing is good. at least on the flip4mac plugin.