Why was Malcolm x murdered?

For being a non-Christian

The ugly facts are that he was murdered by the black Muslims, the Nation of Islam. Malcolm X was a member of the nation. That nation was a vehicle for black nationalism via Islam. But Muslims called them heretics because they were openly and loudly racist. When Malcolm X went to Mecca, he came back a changed man. He rejected racism and began to advocate for civil rights.

It's likely that the 'prophet' Elijah Muhammad resented Malcolm X and saw him as a threat to the organization and its movement. I haven't heard that the assassination was personal.

Thomas Hagan is a former member of the Nation of Islam and one of the assassins who killed Malcolm X in 1965. Hagan stated in a 1977 affidavit, that he had planned the assassination with four others to seek revenge for Malcolm X's public criticism of Elijah Muhammad. He said that one of his accomplices distracted Malcolm X's bodyguards by starting an argument about having been pickpocketed. When the bodyguards moved toward the diversion and away from Malcolm X, a man with a shotgun stepped up to him and shot him in the chest. After that, Hagan himself and another of his accomplices shot several rounds at Malcolm X with handguns.

government wanted him dead

He was murdered by a rival Muslim.