Why did the mob kill Joseph Smith?

The early Mormon Church splintered several times. In 1844, William Law and Robert Foster, disagreed with Smith about how to manage the economy of Nauvoo in Illinois, as well as saying that Smith had proposed marriage to both their wives. They formed a competing church and procured indictments against Smith for perjury and polygamy. On June 7, they published the Nauvoo Expositor, in which they called for reform within the church and appealed to the county's broader community.

Fearing dissent, the Nauvoo city council ordered the press used by Law and Foster to be destroyed by the Nauvoo Legion, an autonomous militia led by Joseph Smith, with the rank of Lieutenant General. Wikipedia explains that destruction of the newspaper provoked a strident call to arms from Thomas C. Sharp, editor of the Warsaw Signal and longtime critic of Smith. Fearing an uprising, Smith mobilised the Nauvoo Legion and declared martial law. A small detachment of the state militia was mobilised and Governor Thomas Ford threatening to raise a larger militia unless Smith and the Nauvoo city council surrendered themselves. Smith and his brother were jailed on a charge of inciting a riot.

A mob stormed the jail and shot both Joseph Smith and his brother Hyrum.

Here are a couple of reasons why Joseph Smith was killed. One, the people that lived in the area of Western Illinois didn't like the Christian beliefs that Joseph believed and was teaching. Two, the citizens of Western Illinois thought if they killed Joseph Smith, the leader of the Church of Jesus Christ of Latter Day Saints (Mormons), all the people following him would pack up and leave. This actually happened, but it was a couple of years later when they did move to Salt Lake City. It wasn't that the mobs were hoping that the Mormons would pack up and leave, they hoped that the religion would fall apart and that Mormonism would be no more.

Other reasons the mob killed Joseph smith include:

• Missouri wanted to become a state of the United States, but wanted to enter the Union as a slave state. Most 'Mormons' tended to be conservative and were against slavery. They were in Missouri in sufficient numbers to sway the vote for Missouri to enter the Union as a "Free State." Therefore, Missouri politics of the day was to either remove Mormons from Missouri or Kill them (by order of the then Governor Boggs). Some especially evil people saw this as Government approval for killing Mormons even if they were not in Missouri.
• Many living on the border of 'Indian Territory' wanted to kill all Native Americans because they were in the way and were considered dangerous. Mormons, on the other hand, were teaching Christianity to the Native Americans, which did not sit well with some Missourians.
• Because there was so much persecution of the Mormons at the time, many Mormons in business, farms, stores, etc. tended to do business with other Mormons mostly, and not so much with non-Mormons. This made some non-Mormons mad.
• Mormons have always practiced the principle of Lay Ministry, other religions of the day did not. Many ministers felt this was a declaration that they were wrong in asking for a wage (of sorts) for doing their ministerial work, and it made 'some' of them angry. Some of these ministers incited people to riot and harm the Mormons.
• Many ministers were of the belief that revelations from God did not occur anymore, once the Bible was 'completed' and both Jesus and his apostles were killed. Joseph Smith was of a different opinion and said he had received further revelation from God. Some ministers took this personally. In their minds it was as though Joseph was calling them liars. He wasn't, he simply disagreed with them.
• Joseph was the leader of the Church of Jesus Christ of Latter Day Saints (or Mormon) Church in his day and this church was very young, compared to most other churches at the time. If Joseph could be killed, it was felt that the Mormon issue would just go away.
• There are many reasons (the above list are just a few), and early-day Mormon Polygamy often caries the sole blame in the minds of some, which is actually a false notion. Polygamy may have been one of the reasons, but not likely the primary reason, nor even one of the more important reasons. Mormons were simply different and being different often attracts the attention of those that have the propensity to do harm.