you have cloned with the wrong command, I guess. Following are the right commands. Notice the first command ends with .git which creates a git directory in which you can run the third command.
git clone git://github.com/ArduPilot/ardupilot.git
git submodule update --init --recursive
Hope that helps.
By the way, I think you posted your question in the wrong place. You should have posted it in here for example.