The difference is simple. Most religions in this world do not take up arms to prove their point. Unfortunately the radical Islamists have done this time and time again. And in some cases have the backing of the government.
In most countries, the governments formulate foreign policies. Governments that are answerable to their people. Unfortunate incidents like Godhra don't get lost in Oblivion.
But if you take the countries ruled with religion as it's main agenda, then things are bound to be tough and in many cases brutal to the people.
That's why Bajrang Dals and Shiv Senas can never come to power in India. But someone like Hizbul Mujahdeen will come to power in an Islamic country.
The Islamic world should stop complaining about the influence of the West. Instead they should be trying to get their people's support. Through dialogue, through people participation, by doing away with stringent rules that gives little or no scope for freedom of thought!!