An atheist writer for The Federalist tells why Islam is far worse than Christianity in this day and age. It may be an atheist perspective, but it's one I can provide with an extension of attention given. He says:
Mohammed was a conqueror who gained worldly political power in his lifetime and used it to persecute opponents and impose his religion. He also fully enjoyed the worldly perks of being a tyrant, including multiple wives. Jesus, by contrast, was basically a pacifist whose whole purpose on earth was to allow himself to be tortured to death.

He even explicitly forbade his followers to use force to defend him. Here’s John, Chapter 18: “Then Simon Peter having a sword drew it, and smote the high priest’s servant, and cut off his right ear…. Then said Jesus unto Peter, Put up thy sword into the sheath: the cup which my Father hath given me, shall I not drink it?”

This does not imply that all Christians ought to be pacifists. But it certainly sets a tone for the religion. The life of the founder of a religion is held up to his followers as a model for how they should live their own lives. The life of Mohammed tells the Muslim that he should expect to rule, whereas the life of Christ tells the Christian he should expect to sacrifice and serve. Which leads us to a deeper doctrinal difference. So despite his stance, he still acknowledges a specific difference between Islam and Christianity's founders. And there's more:
Christians started as a persecuted minority in a pagan society, so that gives them a certain comfort with being powerless. Those who find themselves out of step with the sinful modern world regard this as more or less the normal state of things.

The early history of Islam, by contrast, was further conquest and dominance, as Muslim invaders marched out into Persia and across North Africa. That’s why Muslims tend to look at the modern situation, in which other creeds and political systems are wealthier and wield greater military power, as an aberration that is not to be tolerated.

This history is connected to a specific doctrinal issue. Yes, that's a pretty good observation there too. I don't agree with atheism - I believe there should be distinctions made between good and bad religions - but if you know where to look, you can find some atheists who can raise valid arguments for the right reasons.