Jana, how many times have you traveled to Iran yourself and have witnessed this and how long was the duration of your stay in these trips? You speak as someone with the knowledge of a native (despite the incorrectness).
Whereas in Pakistan there are separate mosques (depending on the Imam) even for those under the Sunni'te school (Ahl-Hadis have different mosques, Deobandi's have their own mosque and etc.. though it's is not as characteristically vivid), such does not exist in Iran. I know of this from personal experience in having lived in Karachi and the Punjab region and because the majority of my Pakistani friends hail from different Sunni'ite schools. In Iran, there is one synagogue irrespective of what denomination of Judaism and there is one church irrespective of what denomination of Christianity. Some groups, for instance, the Armenian Church, represent a greater majority of the Christian minority and thus have more representative churches. The same case follows for mosques. Iran is however itself overwhelmingly Shi'ah and as such the concept of a Shi'ah mosque (or Imambargah as it is popularized in Pakistan) does not exist. As for the Sunn'ite Iranians, they do have their own mosques from where Adhan is called and there is more than one mosque in Tehran also for that matter. The greater number of them are in North-western and south-eastern Iran however as they are better representative of the populations demographically. There are also religious schools for them and they have libraries and their scholars are free to conduct lectures, publish their books and hold religiously orientated gatherings (political gathering are a questionable regardless of religious belief). In any case, any Muslim is able to freely worship as he pleases in any mosque in Iran regardless of the placement of his/her hands. There is much misconception and this is purposely created and quiet annoying for an Iranian.
Iran probably accords much better rights to it's minorities than other Muslim-majority countries from my knowledge and experience. Probably the best amongst them. Furthermore, apart from Jund-shaitan, mosque bombings and so forth are unheard of and Iran is religiously quiet peaceful. As for persecution, all Iranians are persecuted for the same reasons if the persecution happens-- reasons mainly being criminal and political.