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You didn't mention your operating system but for the sake of discussion I'll assume Windows.
The reason it says not to disconnect it is that while it is still communicating with the Library software, there is the possibility that files have not been properly closed yet. If it were to be suddenly disconnected while files are not closed, one or more files could be only partially written, with data still buffered, and detaching the Reader could make a mess of those files.
So, if you're using the Sony software, do what Dreams said. If you're using Calibre, there's a little button for that which appears when you mouse over the device icon. If you're just using Windows Explorer to drag and drop files, you'll want to use the "safely remove hardware" dingus in the system tray.
The same is true, with different details, for *nix. How you dismount the device is specific to your OS, but one way or another, it needs to be dismounted so that all the files are tidied up and all proper housekeeping is done before you physically detach it.
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