Just a bit of my humble (and completely unsubstantiated) opinion on Mr. Mustaine. I read his Wiki page and it says that he was raised Jehovah's Witness. Therein, IMO, lie the seeds of his current views, and also the seeds of his rebellion against religion and subsequent indulgences. It also says that he tried to return the the JW church but didn't care for it anymore.
Also note that his adoption of Christianity coincided with the tumult of his arm injury and the breakup of the Megadeth lineup as it stood at the time. Likely a time of deep reflection. And perhaps bitterness?
The quotes and comments that I've read from him lead me to believe that he's not tremendously intellectual or thoughtful when it comes to politics or religion, and I don't necessarily mean the content of his comments (though I do find them repulsive), I mean the way he phrases them. He speaks like a teenager.