How do I render a video transparent with AE?

Youtube videos show using flv but I do not see that option. I know how to use keylight to make the green screen transparent but can't seem to create the actual video that way.

It's actually called Toggle Transparency grid. It looks like a little checkerboard and it is just left of the Active Camera selector.
NO MEDIA PLAYER will give you a transparent background, it will always look black. A video with an alpha channel will only show up transparent if you bring it into an app that supports alpha channels like AE or Premiere Pro. You cannot have a transparent background in the QuickTime player or in the Windows Media Player. They do not support it.
Did you try the Lossless with Alpha preset? Did you read up on rendering? You cannot just poke around until you get it, you have to read up and understand what you are reading.
If you are trying to render an FLV file for flash then you must use CS6 or earlier. A better approach if you are headed for flash is to render a png sequence with transparency and load that into flash. No matter what you do, embedding a video in a flash file is going to take some bandwidth to play back and it's not going to be compatible with mobile devices. It would really help if we knew what you were trying to accomplish. I still have no idea what kind of product you are trying to get AE to deliver.

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