Here's how: revamping the entire education curriculum, the education system, and of course, by separating religion and state. I'm sure my third point would raise a few eyebrows, but allow me to discuss these points in a bit details.

1. Revamping the education curriculum: I don't know where to start because everything from history and religious studies to science and mathematics needs this. Speaking of science, thanks to the superimposition of religion even over science, our students have absolutely no idea what a scientific method is, how scientific theories are formulated and in a nutshell, what exactly science is. Here's the most common example: Our biology teachers, before beginning to teach evolution in classrooms, clarify that this is "just a theory" and that "it has been proven wrong" and that "of course this is wrong because our religion teaches us that God created Adam and Eve and everything else". Now of course, this is utterly flawed and makes students pretty much averse to science. Although religion should not be dragged into any scientific thinking, but if teachers are adamant on doing this, they should at least have sound knowledge of religion and its relation with science. Our teachers have absolutely no idea that instead of taking Qur'aan literally, it should be interpreted in the light of new emerging knowledge. This has been done my Muslim scholars and philosophers throughout the history of Islam and some scholars even proposed similar views to evolution, even during medieval times. Superimposing religion on science is only destructive and devoids students of the basic mechanism of science. This flaw leads to us generating defective minds in science and technology who support monstrosities like water-car kit etc.

Now to history which is an outrage of its own. The only point our books of "history" (Pak studies) make is that Muslims are and have always remained flawless angels, their every defect and defeat was a consequence of conspiracies by non-Muslims and all the world is out there to hunt Muslims. I recently read the book of Pak Studies prescribed for BA and boy, was I shocked! Other than having about 100 grammatical errors, it utterly lacked in any kind of intellectual content. As per that book, Hindus are pretty much demons who have always conspired against and hated Muslims, and still continue to do so. Even if Muslim Afghanistan was against us during the Zahir Shah regime, according to the book, it was because of Indian and Russian conspiracy.

This mentality results in creating paranoid individuals who see conspiracy in everything happening around us, who have negative and aggressive views about anyone who is not Muslim or anyone who criticizes the rigid interpretations of Islam, and ultimately, in utter intolerance and prejudice.

Bottomline: To cut all this craps from our textbooks, textbooks should be written by respective scholars of the field who have a good reputation, instead of college professors and civil servants who themselves have very limited and superficial knowledge of the fields.

I want to write a lot more on the flaws of education system and curriculum but the above point, I hope, gives an idea.

2. Separation of State and Religion: The current interpretations of Islam are extremely rigid (even medieval Muslim scholars, who we so happily place in our "Golden time" had far more enlightened interpretations). Does anyone around here know who is considered among the fathers of secularism in Europe? Ibn-e-Rushd also known as Averroes. It was the Muslims scholars who, after broadening their horizons with the study of Greek philosophy and others, came up with extremely enlightening interpretations of Quraan and Sunnah while Europe was still deep in the dark ages. The current rigid interpretations of Islam are a direct consequence of the reactionary though emerging out of the Colonisation of Muslim countries (so yeah, a lot of blame does lie on the European colonial powers but that is a different and lengthy discussion).

So the thing is: Secularism is NOT in clash with Islam. Under the state patronage, our so-called "ulemas" have demonized secularism and liberalism so much that these ideas are now considered akin to utter atheism and godlessness in the mind of a common person.

We don't need reactionary and thus rigid interpretation of Islam that only and only promote paranoia and yes, intolerance and prejudice. A religion that was supposed to be for all times and all places should not and cannot be confined within the time frame of the Arabian society as it existed 1400 years ago. It has to evolve with time, just like human consciousness evolves with time, instead of being stale and rigid. Unfortunately, we have long shut the door to the beautiful phenomenon that existed in Islam called "Ijtihad" that allows the interpretation of Qur'aanic teachings in the light of current times.

This second kind of prejudice resulting from religious rigidity, once again, can be overcome with proper, unbiased and authentic education. This, however, seems highly unlikely in at least near future in Pakistan, given the stakes of the state, particularly the military, and of course, the clergy. Pakistan's civil society has to strive for this cause if they seek a better future for their generations, because in any democracy, it's the civil society and media that has always brought about positive changes.