How to configure mongodb replicaset of 3 nodes in authentication mode
You made things in wrong order.
At start you have "open" replica set. You put authorization on and you have so called "localhost exception" what means that you (still) can connect primary directly without authorization. On that connection you MUST first create "root" (super user) user 

use admin
db.createUser(
{
    user: "root",
    pwd: "toor",
    roles: [ "root" ]
})


Now, your "localhost exception" is gone! You must authenticate your self. You can logout and then login again OR just give command 

db.auth("root","toor")

And start creating other (normal) users.