When you have many educated muslims from middle class families posting on defence.pk, supporting a jail sentence for an "aggressive atheist" (whatever that means), then it's no surprise their original country is in a mess tolerance wise where the general population is a lot less educated and a lot more poor.
It may take decades for society to turn more secular but the rise of education, globalisation and the internet will ensure a more tolerant Pakistan (and other "muslim" countries) in the future...hopefully. Until then, unfortunately, it seems that non-believers will have to keep their mouth shut or face persecution and/or jail.