Every religion has broadly three aspects:
Mystical: Pertaining to mythology and supernatural aspects of religion. This could be the basis of creativity as well as of blind faith and non-scientific temper.
Socio-political: Pertains to how the society should behave and be governed. This aspect gives rise to civil and criminal laws and deals with people on an aggregate level.
Philosophical: Pertains to ideas like ethics and morality. The socio-political aspect is in a way dependent on this, after factoring time, and together they form culture.
Now for a religion like Hinduism, all these three aspects are very clearly separable. The philosophical part being most vibrant; giving rise to multitudes of beliefs and schools of thoughts, while the mystical part has helped in development of earliest literature, music, and art forms. The socio-political aspects have been changing with time and with revision of philosophical and reinterpretation of mystical aspects, which is the essence of Hinduism.
Obviously there are some drawbacks also in every aspect too, and some are very serious drawbacks, but a Hindu is free to reject those and yet remain a Hindu.
And this is where ‘problem’ of Islam lies. Islam is seen as a perfect religion to be accepted in totality. One has to submit himself in entirety to this religion, and yes, Islam means ‘submission’.
This notion of it being the ‘perfect’ religion means it is not a ‘pick and choose’ religion like Hinduism. The Muslim has to accept all the aspects and consider them true and final. He can’t reject any aspect. Say, you can’t be a Muslim who would reject the mystical part – e.g. Prophet Mohammad flying on a winged horse – but accept the philosophical or cultural part of Islam.
Even in modern times, these broad three aspects are completely intermingled with each other and almost inseparable; and that causes fundamentalism. The socio-political aspect is stuck in time wrap as you can’t question the philosophical and mystical aspects of the religion – as more often that not, it will be declared blasphemy or apostasy.
But unless Muslims start questioning these and rejecting some of these aspects, including some verses of Quran, nothing will change. Platitudes like everything is right and Islam is just a misunderstood religion won’t help.