I don't judge Islam any more harshly than any other religion, there are aspects of it I truly hate such as making Apostasy a crime, and I find the sexism, homophobia and brutality of Sharia Law disgusting, but other religions have facets I find equally abhorrent (Such as the Jewish concept of circumcision, the idea of unnecessarily mutilating an infants genitals before they are old enough to even decide if they want to follow their parents religion is disgusting. Sure it is harmless and many people have it done by choice anyway, but to make that decision on somebody else's behalf just seems wrong.)

But I have Muslim friends, I judge people by their actions rather than their faith, and know the vast majority of Muslims are good people. The trouble is the Qaran (As with the Torah, the Bible and countless other religious texts) was written in a different age, they are open to misinterpretation and therefore easily exploited by extremists. That's not to say without religion there would be no extremism, but religion gives extremism three massive advantages it would lack without it:

1) The promise of an eternal afterlife makes this life more 'disposable' so people are more willing to die for what they believe their God wants.

2) A country utilising punishments like public floggings would be internationally condemned and sanctioned were they not able to hide behind the cloak of claiming it is in their religion and prejudiced to try to stop it.

3) There will always be small numbers of extremist minorities, but having the leverage of something people hold as dearly as their faith, especially when that faith is based on scriptures that are open to interpretation, gives them an easy way to recruit more people.

As to Islam not being given a fair go, like I said I said it is not just Islam I am against, I mean look at what is been done by Christian hands to Muslims right now in The Central African Republic, and I'm sure if I took the time to look I could find examples both historic and current for just about every religion. I just see religion as a convenient way to explain things that weren't understood in ancient times, but now we have a better understanding of science religion is redundant, and looking back over it's history I would say it has been a catalyst for more tangible harm than good, so serves no purpose in the modern world.