The main reason is the history of the split between the two. When Muhammad was alive, his daughter, Fatima, married Ali (Shiite means "party of Ali). At age 25 Mohammad Married his first wife. All but one if his Children was born to that wife, Khadijah (Mohammad took no other wife as long as Khadijah was alive). Fatima is her daughter, fathered by Mohammad (Khadijah was married two times BEFORE she married Mohammad, and she decided to marry him). Kjadijah was 14 years his Senior in age. At her death Mohammad seems not to have wanted to re-marry, but later did. It appears Mohammad's later marriages either was to take care of widows OR for political reasons (Sometime both). His last wife, and "Favorite" was Aisha, who was the daughter of Abu Bakr (and the only Virgin Wife he took).
I go into the above for it is the background for the split between the Sunni and Shiites. Upon Mohammed's death his followers picked someone other than Ali to succeed Muhammad even through the only child of Mohammad who bore children was Fatima (And Ali was their Father, thus all people who claim descent from Mohammad also are descended from Ali). The Shiites said Mohammad wanted Ali to Succeed him, but the Sunni's said Mohammad wanted his successor picked in the traditional Arab way, by the collection of all his male followers. At the election of Abu Bakr, Ali made his claim but it was rejected and he accepted the decision of the rest of the male followers of Mohammad. Abu Bakr lived less than three years and was succeeded by Umar (Sometimes written as Omar, his full name was Umar ibn al-Khattab"). Umar ruled for 10 years. Umar was succeeded by Uthman ( Full Name Uthman ibn Affan) who ruled for 12 years. Upon an attempted coup by the Arab Governor of Egypt, Uthman was killed and Ali was finally selected as Caliph (Ali would rule for 5 years before being killed). The Killing of both Ali and Uthman appear to be the result of the tribal infighting within the Islamic movement do to all the great wealth it had received since Mohammad's death and the Successive Conquest of Iran, Mesopotamia, Syria, Palestine, North Africa and Egypt. These four Caliphs are consider legitimate Caliphs by the Sunnis. The Shiites believe only Ali should be so considered, but acknowledge Ali did nothing to oppose his three predecessors (Sunnis view this as his acceptance of election as the proper way to select a Successor, Shiites view it was him NOT wanting to shed Moslem blood, which he would have had to do to claim his "right").
After Ali was killed, the family of his predecessor, Uthaman, (the Umayyards,
http://en.wikipedia.org/wiki/Umayyad) took over. The basis for this was accusation against Ali that he was involved with the death of Uthman. The real reason was that Uthman had put as many relatives as he could in the government so that they were the most powerful family within Islam at the time of Ali's death and used that power to take over (Thus inheritance was as important to the Umayyards as it had been to Ali). Ali's son declined to challenge the Umayyards, do to military weakness OR a desire NOT to kill fellow Moslems (Probably both). Thus technically both Shiites and Sunnis worked together at this time period, but the Shiites viewed Ali and his sons as their leader, while the Umayyard ruled as both Political and Religious Leaders. The Umayyards were more into expanding their fortune than expanding their religion (The family had originally OPPOSED Mohammad). This extended to discouraging conversion to Islam, for they preferred to get the higher taxes a non-Moslem paid. They also supported the old Arab families over any new converts (and opposed the Shiites). In 750 AD the Umayyard lost control of the Caliphs to a combination of Enemies, including the Shiites and Persian converts. This installed the Abbasids. The Abbasids were the ones who firmed up the secondary writing so Sunni Religion and turned what had been a top down religion to one of written books (The Shiites had done this since the time of Ali, but those books had been rejected by the Umayyards and Abbasids as NOT supporting they position of power within the Caliphate.
Thus it was not till the 800s that you see a definite split between the Sunnis and Shiites. The Abbasids had scholars find writings that supported their position. Over time the Abbasids became more and more anti-Shiite. A secondary affect of this is that the Shiite adopted a position that one may support whatever Government one is under AND SUPPORT SOMEONE ELSE AS YOUR RELIGIOUS LEADER. At the same time the Abbasid in developing Sunni Islam, adopted a position that the religion and state are one and the same. This is surprising for the Shiites were more exposed to Iranian influence which tended to mix religion and Government up together, while Sunni was exposed to Christianity which had a history of separation between Church and state (More by the Church trying to keep itself independent of the State, then the State becoming independent of the Church).
Since the 800s the Shiites had split into two large groups (They may be others, but small compared to these two groups). The two groups are referred to as the "Sevens" and the "Twelvers". The descendants of Ali had two breaks in their DIRECT linage. One after the death of the Seven Imam (ALi is considered the first) and the other break occurring at the death of the Twelfth Imam. The Twelves are by far the larger of the two groups of Shiites. The Seveners are noted mostly for being the medieval sub-group known as the "Assassins". Most Shiites today ware Twelvers, and given the long history of Suppression by Sunnis, they tend to separate their Government from their Religion much more than Sunnis. When the Iranian Islamic Republic was formed, the Shiite religious leaders had a problem. How do you set up a Shiite Islamic Government. The most successful one in history was the Fatima dynasty in Egypt, but that state was conquered right after the Second Crusade by Sunnis (apparently on a Sunni religious movement in addition to a weak control of Egypt by the Fatimas). The Fatimas had left Sunni religious leaders lead Sunni, as they permitted Christians to lead Christians in Egypt. The Sunni took over and made all Moslem attend Sunni religious program, and while tolerate of Christians, this was to change when the Mamaluks took over after the end of the Third Crusade.
Khomeini thus set up his Islamic Republic, with a Legislature and President elected by the People but from a select group of candidates approved by the Shiite Religious establishment. Furthermore the real power is in hand of the "Supreme Leader" who is the TOP Shiite religious leader in Iran (again selected by the group who decides who can run for President and Legislature). The President is to runt he Country on a day to day basis, but any REAL decision must be made by the "Supreme Leader". Thus the religious leadership does NOT run the Country day to day or even month to month, but had a good say in who makes such decision AND final say in such decision. Many Shiite consider the Islamic Republic of Iran as Heresy, but the best solution on how to set up a Shiite Islamic State (such Shiites are willing to look to other solutions but Iran is the best since the fall of the Shiite Fatima Dynasty of Egypt in the 1200s).
My point here is simple, The Sunnis are into Political and Religious leadership by the same person, who is by definition the leader of both the State and the Church, thus a Sunni Moslem Country the STATE determined both the State and Religious messages to be sent out. That is NOT true of the Shiites. The Shiites believe in a religious hierarchy INDEPENDENT OF THE STATE, which gives such religious leaders the ability to say what Islam is even if that is opposed by the Government. This this Shiite Religious leader is stating something he believes is Islamic Law and as such STRONGER to a Shiite then if the Government had said so.
More on the Umayyards:
http://en.wikipedia.org/wiki/UmayyadMore on the Abbasids:
http://en.wikipedia.org/wiki/AbbasidMore on Fatima:
http://en.wikipedia.org/wiki/Fatima_Zahra More on Umar:
http://en.wikipedia.org/wiki/Umar_ibn_al-KhattabMore on Uthman:
http://en.wikipedia.org/wiki/Uthman_ibn_AffanMore on Ali
http://en.wikipedia.org/wiki/Ali_ibn_Abi_TalibMore on Aisha:
http://en.wikipedia.org/wiki/AishaMore on Khadijah:
http://en.wikipedia.org/wiki/KhadijahFor more on Islam:
http://en.wikipedia.org/wiki/Islam