Yes, because the extremism is rooted in a literal belief in what is written in their "holy" books. More moderate followers of a faith are forced to ignore or directly go against the injunctions of their scriptures.
Well, if you've read the Qur'an, you will know that having fanatics scouring the earth for unbelievers is exactly what Allah wants. The god of the Old Testament is regularly prone to fits of murderous rage, and expressly advocated genocide, among many other atrocities. Intolerance is the cornerstone of Islam, and any literal reading of the Bible will quickly furnish quotes to excuse intolerance and murder as well.
I do agree with the rest of this paragraph, though. If this god is all-powerful, how come they've done such a piss-poor job of communicating with humanity? We do a far better job of communicating our views on this little forum than this god has done- and god's had thousands of years to get it right. And we aren't omnipotent and omniscient. (Well, apart from Jay Utah, of course, who probably is!)
Perhaps, to return to the OP's question, the first thing this supposed returning god should do is explain why they were so crap at explaining what they wanted us to do, and why they were apparently powerless or indifferent to the carnage that has resulted in centuries of internecine fighting, and all-round religion-based unpleasantness. Plus a massive apology, and a promise not to be so crap in the future.