The HC-06 is not a master, it is a slave, and even if it was a master, that isn't the reason why it won't pair with the phone. By far the most likely reason why it won't pair is user error - probably several of them.
I submit the first user error is the refusal to come to terms with the fact that you don't need send any AT commands or MAC addresses in order to establish communication. If you just do that, you at least get to prove there is nothing wrong with the module, the Arduino, the wiring, the code, or the phone, and there was probably no need to order an HC-05 either. As things are, you have no idea if there is anything wrong with any of them, but the chances are good that there is nothing wrong, with the exception of the code, and there is a good chance there is a lot wrong with that. You can prove the code without the bluetooth wired to the Arduino, indeed it is better that it isn't.
Further, there is no evidence of any need to change the configuration after you have proven that your equipment is kosher, and you could be confronted with a dog-chases-car situation if you did change it.
There is some discussion here:http://forum.arduino.cc/index.php?topic=199045.msg1469995#msg1469995
It is possible that the procedures for sending AT commands to the HC-05 and HC-06 are different.
So I realized after a long time that the problem with my last HC-06 was that it was a master device, therefore I couldn't get it to pair with my phone