This is a big subject to get into, but that's quite a statement. As an atheist I would personally argue that pretty much all religious texts are based on a flawed premise. That is not to single out Islam in particular though. That being said, I don't go around saying that to people of faiths, because 99% of people are perfectly reasonable and fine, and I'm not fussed if someone chooses to believe something that I don't, as long as it doesn't have a real impact on me, and I'm certainly not intelligent enough to find the answers. In general I think it is clearly the extremist element that needs to be combatted. There is a poem that I quite like by the mathemetician and poet (among other things) Omar Khayyam, and often think of when you see extremists claiming some form of moral authority. From memory, so apologies.
''And do you think that unto such as you
a maggot-minded, starved, fanatic crew
God gave a secret, and denied it me?
Well, well - what matters it? Believe that too!"