Needs to fallback to transport authentication.

changelog.html

@@ -55,6 +55,8 @@ Upcoming changes</a>
 <!-- Record your changes in the trunk here. -->
 <div id="trunk" style="display:none"><!--=TRUNK-BEGIN=-->
 <ul class=image>
+  <li class=bug>
+    Fixed a bug where SSH public key authentication for CLI wasn't working for username/password based security realm.
   <li class=rfe>
     Added a dignosis CLI command to report the current granted authorities.
 </ul>

core/src/main/java/hudson/security/AbstractPasswordBasedSecurityRealm.java

@@ -64,7 +64,7 @@ public abstract class AbstractPasswordBasedSecurityRealm extends SecurityRealm i
 
             public Authentication authenticate() throws AuthenticationException, IOException, InterruptedException {
                 if (userName==null)
-                    return Jenkins.ANONYMOUS;    // no authentication parameter. run as anonymous
+                    return command.getTransportAuthentication();    // no authentication parameter. fallback to the transport
 
                 if (passwordFile!=null)
                     try {