The same can be asked to the Muslim extremists.
If God is in fact the creator, he can do as he see's fit. If you look at it like that, its one of those if I built it, I can destroy it, type things. I'm sure as a kid your parents said to you at some point or you've heard it, "I brought you into this world and I can take you out". Now that isn't in the literal sense (in most cases) but if God does exist I'm sure that is the way that it works. Many of the reasons thousands of people get killed in the bible have very clear reasoning behind them. There is no secret that God can be merciful, but no where in the Bible does it state that he is generally a merciful God. If you believe, you are supposed to live by his code of ethics placed in the Bible. If you do not you are sent to burn in Hell for eternity. There doesn't sound like theres much mercy in that, if you ask me.
Don't get me wrong, I am a Christian. A baptist infact. I have read through the Bible, I haven't finished it and don't claim to have. But I respect all points of view like it is asked of me in the Bible.
There is, however, one point of view that I cannot see eye to eye on, Muslim extremism. I know plenty of good people who are Muslim, but the extremists are generally the ones who commit martyrdom. Examples being 9/11 and stoning people inside of generally Muslim countries for dis-obeying the Muslim religion. In the Bible, God justifies his own killings, but asks that the people not do it for him. It is considered a sin, against the Biblical religious code.
I haven't looked much into the religion of Islam so I'm not quite sure what that pertains to in scope of all this.
Anyway, thats my look at it. I'm not bashing the Muslims nor am I justifying any killings what so ever. Its not my place to do so.