Two-factor authentication is an extra layer of security for your Apple ID designed to ensure that you’re the only person who can access your account, even if someone knows your password. Apple is now requesting this method for using his services; such as: signing in to their Apple Developer account and Certificates, Identifiers & Profiles.
This authentication can cause however login issues with some apps. The Application Loader is an example. This app is very useful to publish app coming outside Xcode process (e.g. phoneGap, HTML5 apps).
A good solution is the temporary password generation from appleid account management: https://appleid.apple.com/account/manage
In the security section you will be able to set up a temporary password (specific password for app). An input with a name to fill will popup and a password will be showed on the screen after.
You will be able to login after with your iTunes email and the temporary password given.