The root cause of anti-Shia violence perpetrated by militantly sectarian and mostly Wahhabi/Salafi minded elements within the Sunni muslims is the existence of major misconceptions regarding Shia muslims. This goes as far as considering Shias „non-muslims“ (Kuffar) or worse „apostates“ (Murtadeen).

Hateful incitements against the Shias have been „explained“ by takfiri ideologues using a wide array of mostly unsustainable religious pseudo-arguments in order to justify and „legitimize“ the killing of Shia muslims.
Thus it is time to identify and refute these deadly misconceptions.

The misconceptions:

1. There is a „Shia Quran“ which is different than the „Quran“
Truth: Of course there is no such seperate and different Quran. The Quran sold and read in Tehran is the same as in Riyadh.

2. The Shia believe that Imam Ali (ibn Abi Taleb, cousin and son-in-law of Prophet Mohammad) is „God“
Truth: No Shia Imam or scholarly person has ever claimed this and this is also totally inconsistent with the „Shahada“ formula that every practising Shia uses: „La ilaha illa Allah wa-Muhammad rasul Allah. There is no god but God and Muhammad is the prophet of Allah. “

3. The Shia believe that archangel Gabriel (Jibr´eel) „mistakingly“ gave prophethood to Prophet Mohammad instead to Imam Ali
Truth: Same as with misconception 2

4. The Shia do not pray 5 times a day and a total of 17 Rakaat
Truth: „In Shia mosques, whether in Iran or the USA, all five daily prayers are performed. Shia do combine noon and afternoon and evening and night, but Shia scholars recommend performing them separately.“
http://www.ezsoftech.com/akram/shiasunniunity.asp

5. The Shia do not pray voluntary „Sunnah“ prayers (in addition to the obligatory „Fard“ prayers)
Truth: Beside the fact that the „Sunnah“ prayers are voluntary and thus NOT compulsitory, „Shias do perform non-obligatory prayers, 36 cycles per day in total, but call it Nawafil and not Sunnah.“ For details, see here: http://en.wikipedia.org/wiki/Salat

6. Lying and deception is allowed for the Shia because they make use of „Taqiyyah“ (Dissimulation)
Truth: Shias are of course not allowed to lie or deceive or give wrong testimony. „al-Taqiyyah literally refers to the practice of hiding one’s faith when one’s life is in danger from others who may wish to harm them for what they believe…Muslims should employ the practise of Taqiyyah in matters of life and death. In reality the Shia have found themselves in that very situation on numerous occasions throughout Islamic history.

The practice is legitimised during times of danger by the Holy Qur’an in Surah 16: Ayah 106:

 “Whoever renounces faith in Allah after {affirming} his faith—barring someone who is compelled while his heart is at rest in faith—but those who open up their breasts to unfaith, upon such shall be Allah’s wrath, and there is a great punishment for them.”

This verse was revealed in relation to the Prophet’s (s.a.w) companion ‘Ammar b. Yasir, after he was forced to use renounce his faith in order to save his life from the Qurayshi pagans who were torturing and killing Muslims for refusing to outwardly profess disbelief.“
http://shiastudies.org/article/taqiyyah
Though Sunni muslims do not use the word „Taqiyyah“, the concept as such is not unknown: http://en.wikipedia.org/wiki/Taqiya#Sunni_Islam_view

7. Shias are „polytheists“ because they worship others than Allah
Truth: No, of course Shias only worship Allah. They have been accused of „shirk“ because of prostrating on a piece of earth (clay) during the prayer. This has nothing to do with polytheism (by „worshipping stones“) as Sunni Sheikh Ahmed Deedat explains here very well:

“An example is that the Shia brothers when they make salat, they have a piece of clay (turbah) that they do sajjdah on. And he( Sunni cleric) says, “see what they are doing here. This is shirk. They are worshipping a piece of clay.”
I said why don’t you ask them why they place their foreheads on a piece of clay and learn the logic behind this. I asked them. Why do you carry this clay tablet everywhere you go in your pocket? They said “we are supposed to do sujood on Allah’s earth with our foreheads touching the earth. We say “subhanna rabia Allah” three times with our foreheads touching the earth.” So the Shia want to actually touch the earth with their foreheads and not a manmade carpet. They want to be true to the expression of praying with the forehead actually touching Allah’s earth. You see they don’t worship the clay tablet as many wrongly think. And this is always something that we Sunnis are always making fun of and mock the Shia.”“  https://revivinghope.wordpress.com/tag/shia-sunni-unity/

At times, Shias visiting shrines have been wrongfully accused of „worshipping“ the (graves of the) dead.
„Touching or kissing the shrines of the Prophet and the imams does not imply shirk, nor does it associate that particular person with Allah, because Allah has the ultimate sovereignty in this universe, and Muslims submit to, worship, and seek help only from Him. Visiting the shrines is merely a gesture of respect.“

The Noble Qur’an teaches that when Prophet Yaqub cried over the separation of his son, Yusuf he lost his eye sight. Years later, Yusuf sent his shirt with one of his brothers and told him to put it on the face of his father so that he would regain his sight. The Qur’an says:

„Go with this shirt of mine and cast it over the face of my father. He will become seeing. And bring to me all your family. And when the caravan departed (Egypt), their father (who was in Palestine) said, “I do indeed sense the smell of Yusuf, if only you think me not sane.” They (his family) said, “Certainly you are in your old error.” Then when the bearer of glad tidings arrived, he cast it (the shirt of Yusuf) over his face, and he became seeing. He said, “Did I not say to you that I know from Allah that which you know not?”[Quran, 12:93]

Today, in most countries, both Muslim and non-Muslim, the flag of a nation is so sacred that soldiers, even civilians kiss it and put it on their faces. Does that mean they are worshipping a piece of cloth?
http://allaboutshias.com/shias-view-on-grave-worship/

8. Self-flaggelation is part of Shia ideology
Truth: No, it is not part of the ideology and even less a core belief of Shiism. Unfortuntaly it is still practised by many thousands of Shias but it should be noted that the broad majority of Shia does not commit it:
„Fatwa by the supreme leader of Iran – The Shia majority Iran and many Shiite clerics have denounced self-flagellation as un-Islamic and have issued a fatwa banning self-flagellation. The fatwa has led to many Muslims denouncing self-flagellation and have instead organized blood donation camps. Some have ignored the fatwa…With many Shiite clerics denouncing the act of self-flagellation, the act of self-flagellation is more of an Asian phenomenon now more particularly India & Bangladesh.“
http://thelogicalindian.com/story-feed/opinion/this-blood-soaked-islamic-ritual-needs-to-be-banned-completely/

Also: „Suffering and cutting the body with knives or chains was banned by Ali Khamenei, Supreme Leader of Iran and by Hezbollah in Lebanon.^[62] Khamenei issued a fatwa on 14 June 1994 banning this practice. He considered it irreligious and not suitable for good Muslims.“
https://en.wikipedia.org/wiki/Criticism_of_Twelver_Shia_Islam#Mourning_Husayn_and_self-flagellation_during_Ashura

9. Shias hate or insult the Prophets companions (Sahaba)
Truth: While, it is unfortunately true that some Shia indeed (have) insult(ed) some of the Sahaba, it is unfair and incorrect to accuse the Shia collectively of doing this. This shameful „habit“ is also nothing that is part of the general upbringing or education of an average Shia.
More interestingly, it should be noted that Ayatollah Khamenei from Iran strictly forbids insulting the Sahaba:
http://www.sunniandshia.com/unity-between-shia-and-sunni-on-imam-khameneis-fatwa/
Also: „Shia consider the first three caliphs as great companions and good Muslim administrators, but not spiritual leaders (imams). Imam Jafar Sadiq, whose mother and grand mother came from the line of Abu Bakr, said of Abu Bakr, “He gave me birth twice.” Ayisha is respected by Shias as the „Mother of Believers,” as Ali respected her when he sent her back from Basra to Madinah after the Battle of the Camel. If some Shia do slander the three caliphs and Ayisha, they do it out of ignorance and should ask God’s forgiveness.“
http://www.islamicity.org/2237/sunni-misconceptions-about-shias/

„Ayatollah Ali al-Sistani’s fatwa in October 2013, when he strictly forbade attacking Sunni sanctities, stating, “These are condemnable acts, and they violate the Shiite imams’ orders.”…Several Shiite authorities cooperated with Tayeb’s latest request and issued several fatwas and statements forbidding insulting Sunnis.“
http://www.al-monitor.com/pulse/originals/2015/01/iran-iraq-fatwa-sunni-shiite-insults.html#

10. Shias practice temporary marriages (Mutah) 
„Temporary marriage (Mutah) was allowed during the time of Prophet Muhammad (pbuh) and he himself practiced it. Ibn Zubayr was born out of a temporary marriage. Later on Caliph Umar prohibited it due to social reasons as the Islamic world was rapidly expanding. Shias discourage Mutah but do not consider it prohibited. “
http://www.al-islam.org/muta-temporary-marriage-in-islamic-law-sachiko-murata/legitimacy-muta

Instead of pointing at alleged or real differences the focus should be put on highlighting the common ground:

„Shia and Sunni have many things in common. They both believe in One God (Allah), follow the same Prophet Muhammad (pbuh) as the last Prophet, offer five daily prescribed prayers, perform the prescribed fast in the month of Ramadan, go to Makkah for the Hajj pilgrimage, read the same book of Allah, Holy Qur’an, and pay the poor-due (Zakat).“
http://www.ezsoftech.com/akram/shiasunniunity.asp
In addition, both Shias and Sunnis share the most important holidays: Eid al adha and eid al fitr