The question above stems from two other questions:

First: Do Shias truly believe that all but a few of the Sahabah were infidels and hypocrites?

Second: Why didn't the majority take advantage and get rid of the rest by killing them?

Regarding the first question if what is meant by infidelity is worshiping idols and statues, Shias do not believe that the majority of the sahabah were infidels and disbelievers. As a matter of fact among the hundreds of thousands of believers few actually denounced their faith and returned to worshiping idols like before. But it must be noted that the terms hypocrisy and infidelity refer to other meanings too. In the Tafsir of Ebn-hatam

We read that before the emerge of Islam severe conflicts occurred between the two tribes of Oos and Khazraj that were resolved after embracing the Islam, years later the same conflicts were brought up and once again the two tribes were mad and upset at each other causing them to want to go to war against each other, then the one hundred and first verse of surah Ale-Imran was revealed, the verse says: And how would ye deny faith while unto you are rehearsed the Signs of Allah, and among you lives the Messenger. Whoever holds firmly to Allah will be shown a way that is straight.[1]

Although the two mentioned tribes never truly became disbelievers the quran has used the term of infidelity (kufr) to describe their act.  We also find instances of such a thing in other verses[2].  The term hypocrite (munafeg) doesn't refer only to people like Abdullah ibn-e- obey (a hypocrite that lived at that time)

that were well known to be hypocrites but also refers to those of the hypocrites who even the prophet could not recognize despite his clever.  There some of them that only god knew about[3]. Even the term(apostate) can refer to different meanings. The twenty first verse of surah Al-Imran and the verses that follow it show that Bani esrael had turned away from Judaism in some ways but not that they had truly denounced their faith and actually embraced the religion of their ancestors. After all it must be noted that shias believe the Sahabah committed sins and the term infidels can be used for them the same way god has used it for the abovementioned tribes, and as explained they did not  actually denounce their faith and worship idols.

The answers number 3501,3275,2982,1970 and 1167 are related to what was mentioned.

But regarding the second question that why didn't the majority take advantage and get rid of the rest by killing them, we will mention a few examples and then taking the verses in to consideration we will mention the appropriate response to this question:

1- Some verses in the Quran assert that prophet Noah called his people for almost 950 years to worship god[4], and during this long period not many joined him[5], according to sunni tafsirs and at the highest estimation the number of those who embraced the new religion didn't exceed 100[6]. The question that comes to mind is why didn't the majority of disbelievers demolish this small group?

2- Why is it that prophet Aaron survived when the majority of Bani-Esrael where misguided by sameri [7] and the prophet was close to be killed[8]?

3- When prophet Moses was not obeyed by bani-esrael he complained to god in his prayers that he had no control over any one other than himself and his brother. Due to his complaint god banished them for forty years which they spent in the deserts and has referred to everyone but the two prophets by the term (corrupt)[9]. How come the corrupt individuals never killed prophet Moses and Aaron?

4- When the followers of prophet Jesus disobeyed him and he felt disbelief in them[10] and only some of the apostles (12 of them) responded to his call[11], why wasn't the group of twelve apostles and the prophet himself killed and how come Christianity wasn't abolished to later on dominate the world?

5- How did our prophet survive for 13 years in the two cities of Mecca and Medina during the advent of Islam when he barely had any companions? How did he manage to immigrate to habasha in such a situation for his word to be spread around the globe?

It seems that taking these verses (that all Islamic sects agree on) in to consideration there is no question left to be answered, because there are so many examples of such a situation that took place before it happened for Ali and his companions.  There are numerous examples of societies in which prophets had very little companions and even though the majority had either never joined the prophet or had renounced their faith afterwards, the prophets survived and lived to spread their word and call. Add to all above that when mentioning the infidelity of the Sahabah in some hadiths (if they are authentic) what is meant is the state of committing sins, not that they completely turning away from Islam.

It seems that even though some of the Sahabah stayed Muslims after the death of the prophet, they didn't follow some of his teachings due to the lifestyle they were used to before the emerge of Islam, and also didn't obey the prophet regarding the very important issue of Khilafa and this resulted in an argument that has been going on ever since.

When prophet Moses prayed to god that no one but his brother will obey him, he did not mean that all of bani-esrael had become disbelievers. What was meant was that all of them would not follow his orders regarding critical issues and matters that would affect the society's future , for example they were suppose to enter the holy land but they didn't and as a result they ………………..in the deserts. It goes the same about the Islamic society back then, unfortunately the Sahabah didn't act according to the prophets guiding about his successor, and never gave Ali (pbuh) the chance, knowing that the he was like an brother to prophet the same way Aaron was to prophet Moses[12]. What the Sahabah did was literally the same as what Bani-Israel did, the Sahabah put Ali (pbuh) aside knowing all of what he had done and what he had gone through for the sake of Islam, therefore the people could not benefit from him, and this prevented Muslims from reaching salvation /prosperity.

It must be noted that usually the majority of a society does not get rid of the group which disagree with them by physical ways, but engage in the battle by putting them aside so that they will not attract attention and will be forgotten.

Surely the group that took over after the prophet was clever enough to realize that killing Ali (pbuh) and his few followers would lead to them being overthrown, because although the majority didn’t support Ali (pbuh), but they were aware of his high status and the sacrifices he had done for the sake of Islam. Therefore they decided to go on without martyring him. There were times when the government would come upon problems and crises and would ask him for guidance and help, despite the great disagreements and differences in viewpoints they had.

Later on many of the Sahabah made up for their acts and fought along with Ali (pbuh) against the Marigin, Nakesin and Gasetin.

After the emerge of Islam the society had undergone so many changes and had become different in so many ways that even if one intended to return to the past age in lifestyle and turn away from Islam, he/she could not bring up the idea and talk about it.  Therefore all of those who ruled after the mentioned changes claimed that they were Muslims even though they didn't act according to Islam's teachings. Rulers like Yazid never said that they didn't believe in Islam but would drink wine publicly and literally violate all laws of Islam.  We still see people that rule Islamic countries and attend Islamic gatherings and consider themselves Muslims, despite the fact that they break Islamic laws and violate them.

Therefore one can conclude that the fact that Ali (pbuh) was not martyred and that the majority didn't renounce their faith does not contradict the Shias belief that most ahabah were not righteous and committed sins.