This is the behavior of ln if the second arg is a directory. It places a link to the first arg inside it. If you want /etc/nginx to be the symlink, you should remove that directory first and run that same command.
That's what ln is documented to do when the target already exists and is a directory. If you want /etc/nginx to be a symlink rather than contain a symlink, you had better not create it as a directory first!