Because he put himself above God and His Holy Church. He got rid of Scriptures that contradicted his beliefs, such as II Mach. 12:46, 'It is, therefore, a holy and wholesome thought to pray for the dead, that they may be loosed from sins.'
From the National Catholic Register
By Angelo StagnaroAmid all the damage Martin Luther did in rending the body of Christ, perhaps his most deeply ingrained legacy is his shortened canon of Scriptures.
Many people seem to believe Catholics “added” books to the Bible. They don’t seem to realize that Luther removed seven entire books and parts of three others from it for no other reason than that they didn’t fit his idea of “what God really wanted.” Luther claimed they celebrated Judaism and because he wanted to justify his challenging the authority of the Catholic Church, he threw them out.
The Protestant Bible consists of only 66 books ― 39 books in the Old Testament and 27 books in the New Testament. The Catholic (i.e., the original canon) settled upon in the 4th century is contains 73 books including Tobias, Judith, Wisdom, Sirach (i.e., Ecclesiasticus), Baruch, and 1 and 2 Maccabees ― what Protestants call the Apocrypha.
In fact, Luther’s first German translation was missing 25 books (i.e., Genesis, Exodus, Leviticus, Numbers, Deuteronomy, Esther, Job, Ecclesiastes, Jonah, Tobias, Judith, Wisdom, Sirach (i.e., Ecclesiasticus), Baruch, 1 and 2 Maccabees, Matthew, Luke, John, Acts, Romans, Hebrews, James, Jude and Revelation. He referred to the Epistle of James as “straw not worthy to be burned in my oven as tinder.” The rest he called “Judaizing nonsense.” Subsequent Protestants, deciding that Luther wasn’t really inspired by the Holy Spirit, replaced most of the books he had removed.
In the third and fourth century, amid a flurry of gnostic nonsense producing dubious gospels left and right, the Council of Nicaea met to determine which books were canon. Some of them were easy to detect. The Gospel of Thomas quoted Jesus as saying that women can’t get into Heaven. The Infancy Gospel according to St. Thomas had a particularly gruesome scene in which the young Jesus killed his little playmates. These stories are, at the very least, uninspired and uninspiring.
The major problem lay with the Old Testament which Jewish scholars limited to 39 books. However, there was also a Greek Old Testament (i.e., the Septuagint) which contained these 39 books and others. All of the New Testament writers wrote in Greek and thus used the Greek Septuagint as source material. The learned scholars and saints who assembled the Bible the Church has preserved believed the Scriptures were divinely inspired. If such were the case, the authors couldn’t have used the wrong source ― that would be ludicrous. Thus, the council wisely included the Septuagint in the books of the Christian Bible rather than the Hebrew Masoretic text.
Luther argued that the Catholic Church had no right to decide matters of canonicity, completely disregarding the fact that he had awarded himself that very right. He held that the internal worth of a book was the chief factor in deciding if it should be kept or not. This argument is silly, because Judaism obviously doesn’t recognize the 27 Christian books either.
Luther’s mistakes are obvious. The reformer’s intention wasn’t to get at the truth of the Scriptures but rather to edit out the “messy parts” that contradicted his new vision of Christianity. So why would anyone trust a man who hated all Jewish references in the Bible so much that he singlehandedly corrupted it?
Though the Hebrew Bible that Jesus read didn’t include these books, he referred to them in his ministry. The New Testament we have today is completely dependent upon the Septuagint and thus, for the sake of continuity, historicity and authenticity, Luther should have kept his unauthorized editing to himself.